Phenylpropanoid related regulatory protein-regulatory region associations

ABSTRACT

Materials and methods for identifying lignin regulatory region-regulatory protein associations are disclosed. Materials and methods for modulating lignin accumulation are also disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority under 35 USC §119(e) to U.S. Provisional Patent Application Ser. No. 60/854,825, filed on Oct. 27, 2006, the entire contents of which are hereby incorporated by reference.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

Funding for the work described herein was provided by the federal government (U.S. Department of Energy Grant No. DE-FG02-05ER64111), which has certain rights in the invention.

INCORPORATION-BY-REFERENCE & TEXTS

The material on the accompanying diskette is hereby incorporated by reference into this application. The accompanying compact discs contain one file, 11696231001SequenceListing.txt, which was created on Oct. 29, 2007. The file named 11696231001SequenceListing.txt is 5,719 KB. The file can be accessed using Microsoft Word on a computer that uses Windows OS.

TECHNICAL FIELD

This document relates to materials and methods for modulating expression of nucleic acid sequences of interest, including both endogenous and exogenous nucleic acid sequences, such as those involved in phenylpropanoid (e.g., lignin) biosynthesis. For example, this document provides materials and methods for identifying regulatory protein and regulatory region pairs, e.g., transcription factor-promoter pairs, as well as materials and methods for using such associated pairs to modulate (e.g., increase or decrease) lignin content in plants.

BACKGROUND

Phenylpropanoids are plant-derived organic compounds that are biosynthesized from the amino acid phenylalanine. Intermediates and end products of this pathway include compounds having important roles in plants, such as phytoalexins, antiherbivory compounds, antioxidants, ultra-violet protectants, pigments, and aroma compounds. Many of the components derived from this pathway such as flavonoids, flavonols, isoflavones, and anthocyanins are known to have nutritional value and are believed to prevent cardiovascular disease, cancer, diabetes, and other diseases related to oxidative stress. The majority of the carbon in the phenylpropanoid pathway is channeled toward the synthesis of lignin. As the second most abundant polymer on earth, exceeded only by cellulose, lignin is a major carbon sink in the biosphere, accounting for about 30% of the carbon sequestered into terrestrial plant material each year (Battle et al., Science, 287:2467 (2000)).

Lignin is a major structural component of secondarily thickened cell walls of tissues with conducting and/or mechanical functions. Angiosperm lignin is composed of three main units named p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) units. These components originate from the polymerization of three monolignols, p-coumaryl, coniferyl, and sinapyl alcohols, respectively. The monolignols are synthesized from phenylalanine through successive deamination, reduction, hydroxylation, and methylation steps. The proportions of H, G, and S units in the cell wall vary according to plant species and tissue type.

As a major polymer of cell walls, lignin has a direct impact on the characteristics of plants and plant products, such as wood. Highly lignified wood is durable and therefore a good raw material for many applications. Since lignin yields more energy when burned than cellulose, lignified wood is also an excellent fuel. The mechanical support provided by lignin prevents lodging, a problem in many agronomically important plants. On the other hand, lignin is detrimental to paper manufacture and must be removed from pulp before paper can be manufactured. This is costly both in terms of energy and the environment.

Lignin also makes it difficult to break down biomass for conversion into cellulosic ethanol biofuel. Cellulosic ethanol, which exhibits a net energy content three times higher than corn ethanol, can be produced from a wide variety of cellulosic biomass feedstocks including agricultural plant wastes, plant wastes from industrial processes and energy crops grown specifically for fuel production. Cellulosic biomass is composed largely of cellulose, hemicellulose and lignin, with smaller amounts of proteins, lipids and ash. Processing cellulosic biomass aims to extract fermentable sugars from the feedstock, which requires disruption of the hemicellulose/lignin sheath that surrounds the cellulose in plant material. Technological developments that increase the yield and drive down the production cost of cellulosic ethanol can help to reduce our oil dependency in a sustainable way. Given the role of lignin in the recalcitrance of biomass for conversion to biobased fuels, in addition to the many other roles of lignin, it is desirable to have the ability to produce plants with modulated levels of lignin.

SUMMARY

The present invention relates to materials and methods for modulating expression of nucleic acid sequences, such as those encoding polypeptides involved in phenylpropanoid (e.g., lignin) biosynthesis. For example, the invention relates to the identification of regulatory proteins that are associated with regulatory regions, e.g., regulatory proteins that are capable of modulating expression of nucleic acid sequences that are operably linked to regulatory regions from genes encoding enzymes involved in lignin biosynthesis. Modulation of expression can include up-regulation or activation, e.g., an increase of expression relative to basal or native states, e.g., a control level. In some cases, modulation of expression can include down-regulation or repression, e.g., a decrease of expression relative to basal or native states, such as the level in a control. In many cases, a regulatory protein is a transcription factor and its associated regulatory region is a promoter. Regulatory proteins identified as being associated with regulatory regions of genes encoding enzymes involved in lignin biosynthesis can be used to create transgenic plants such as trees having increased amounts of lignin in thickened secondary cell walls to sequester carbon, and biomass energy crops having decreased lignin to improve the efficiency of conversion to ethanol. Such plants can have modulated, e.g., increased or decreased, amounts and/or rates of biosynthesis of lignin. In addition, the structure and/or composition of lignin produced by such plants can vary from that produced by corresponding wild-type plants. Regulatory proteins can also be used along with their cognate promoters to modulate expression of one or more endogenous sequences, e.g., lignin biosynthesis genes, in a plant cell. Given the many functions of lignin, it would be useful to control selective expression of one or more polypeptides, including enzymes, regulatory proteins, and other auxiliary polypeptides, involved in lignin biosynthesis, e.g., to regulate biosynthesis of one or more lignin monomers, or monolignols, and/or to regulate polymerization of lignin monomers into lignin.

Reducing the lignin content in dedicated energy crops such as switchgrass can improve the yield and facilitate the production of ethanol from cellulosic feedstock. Reducing lignin in forage crops such as alfalfa can improve the quality and digestibility of such crops. In trees, a reduction in lignin content can improve paper pulp production. Increasing the lignin content in plants can also be useful. For example, increasing lignin in plants can enhance long-term carbon sequestration in plant biomass, which, in turn, may reduce atmospheric carbon dioxide and global warming. An increased lignin content can also prevent plant lodging, make vegetables more firm and crunchy, enhance the fiber content of foodstuffs, confer plants with improved pathogen resistance, and increase the amount of energy that can be obtained by burning wood.

In one aspect, a method of producing a plant is provided. The method comprises growing a plant cell comprising an exogenous nucleic acid. The exogenous nucleic acid comprises a regulatory region operably linked to a nucleotide sequence encoding a polypeptide. The Hidden Markov Model (HMM) bit score of the amino acid sequence of the polypeptide is greater than about 20, using an HMM generated from the amino acid sequences depicted in one of FIGS. 1 to 51 or 53 to 131. The plant has a difference in lignin content as compared to the corresponding lignin content of a control plant that does not comprise said nucleic acid.

In another aspect, a method of producing a plant is provided. The method comprises growing a plant cell comprising an exogenous nucleic acid. The exogenous nucleic acid comprises a regulatory region operably linked to a nucleic acid encoding a polypeptide. The polypeptide comprises a polypeptide sequence having 80% or greater sequence identity to a polypeptide sequence selected from the group consisting of SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, SEQ ID NO:2087, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, and SEQ ID NO:2348; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

In a further aspect, a method of producing a plant is provided. The method comprises growing a plant cell comprising an exogenous nucleic acid. The exogenous nucleic acid comprises a regulatory region operably linked to a nucleotide sequence having 95% or greater sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:118, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:129, SEQ ID NO:133, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:148, SEQ ID NO:150, SEQ ID NO:156, SEQ ID NO:158, SEQ ID NO:160, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:169, SEQ ID NO:171, SEQ ID NO:177, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:271, SEQ ID NO:274, SEQ ID NO:278, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:314, SEQ ID NO:317, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:327, SEQ ID NO:329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:336, SEQ ID NO:338, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:352, SEQ ID NO:354, SEQ ID NO:356, SEQ ID NO:360, SEQ ID NO:369, SEQ ID NO:371, SEQ ID NO:373, SEQ ID NO:376, SEQ ID NO:378, SEQ ID NO:380, SEQ ID NO:386, SEQ ID NO:390, SEQ ID NO:393, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID NO:416, SEQ ID NO:431, SEQ ID NO:435, SEQ ID NO:437, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:444, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:453, SEQ ID NO:458, SEQ ID NO:460, SEQ ID NO:464, SEQ ID NO:469, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:477, SEQ ID NO:482, SEQ ID NO:486, SEQ ID NO:489, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:500, SEQ ID NO:503, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:515, SEQ ID NO:517, SEQ ID NO:519, SEQ ID NO:523, SEQ ID NO:525, SEQ ID NO:528, SEQ ID NO:534, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:544, SEQ ID NO:547, SEQ ID NO:552, SEQ ID NO:554, SEQ ID NO:562, SEQ ID NO:565, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:573, SEQ ID NO:577, SEQ ID NO:580, SEQ ID NO:582, SEQ ID NO:584, SEQ ID NO:589, SEQ ID NO:592, SEQ ID NO:595, SEQ ID NO:598, SEQ ID NO:600, SEQ ID NO:602, SEQ ID NO:605, SEQ ID NO:607, SEQ ID NO:609, SEQ ID NO:611, SEQ ID NO:613, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:637, SEQ ID NO:649, SEQ ID NO:651, SEQ ID NO:655, SEQ ID NO:658, SEQ ID NO:660, SEQ ID NO:664, SEQ ID NO:670, SEQ ID NO:674, SEQ ID NO:677, SEQ ID NO:679, SEQ ID NO:681, SEQ ID NO:683, SEQ ID NO:685, SEQ ID NO:688, SEQ ID NO:694, SEQ ID NO:697, SEQ ID NO:699, SEQ ID NO:702, SEQ ID NO:704, SEQ ID NO:706, SEQ ID NO:708, SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:717, SEQ ID NO:719, SEQ ID NO:721, SEQ ID NO:723, SEQ ID NO:729, SEQ ID NO:736, SEQ ID NO:741, SEQ ID NO:743, SEQ ID NO:746, SEQ ID NO:752, SEQ ID NO:754, SEQ ID NO:759, SEQ ID NO:764, SEQ ID NO:778, SEQ ID NO:780, SEQ ID NO:785, SEQ ID NO:789, SEQ ID NO:792, SEQ ID NO:795, SEQ ID NO:797, SEQ ID NO:799, SEQ ID NO:801, SEQ ID NO:807, SEQ ID NO:810, SEQ ID NO:813, SEQ ID NO:815, SEQ ID NO:819, SEQ ID NO:821, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:829, SEQ ID NO:832, SEQ ID NO:834, SEQ ID NO:837, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:848, SEQ ID NO:851, SEQ ID NO:854, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:864, SEQ ID NO:867, SEQ ID NO:884, SEQ ID NO:889, SEQ ID NO:891, SEQ ID NO:893, SEQ ID NO:895, SEQ ID NO:897, SEQ ID NO:899, SEQ ID NO:903, SEQ ID NO:906, SEQ ID NO:911, SEQ ID NO:913, SEQ ID NO:916, SEQ ID NO:918, SEQ ID NO:920, SEQ ID NO:926, SEQ ID NO:928, SEQ ID NO:933, SEQ ID NO:935, SEQ ID NO:937, SEQ ID NO:942, SEQ ID NO:944, SEQ ID NO:958, SEQ ID NO:963, SEQ ID NO:965, SEQ ID NO:967, SEQ ID NO:972, SEQ ID NO:974, SEQ ID NO:979, SEQ ID NO:981, SEQ ID NO:993, SEQ ID NO:1006, SEQ ID NO:1010, SEQ ID NO:1015, SEQ ID NO:1027, SEQ ID NO:1030, SEQ ID NO:1034, SEQ ID NO:1049, SEQ ID NO:1051, SEQ ID NO:1054, SEQ ID NO:1057, SEQ ID NO:1059, SEQ ID NO:1061, SEQ ID NO:1063, SEQ ID NO:1067, SEQ ID NO:1070, SEQ ID NO:1077, SEQ ID NO:1080, SEQ ID NO:1082, SEQ ID NO:1084, SEQ ID NO:1086, SEQ ID NO:1090, SEQ ID NO:1093, SEQ ID NO:1095, SEQ ID NO:1097, SEQ ID NO:1103, SEQ ID NO:1108, SEQ ID NO:1116, SEQ ID NO:1121, SEQ ID NO:1124, SEQ ID NO:1128, SEQ ID NO:1130, SEQ ID NO:1133, SEQ ID NO:1135, SEQ ID NO:1138, SEQ ID NO:1142, SEQ ID NO:1148, SEQ ID NO:1155, SEQ ID NO:1158, SEQ ID NO:1160, SEQ ID NO:1162, SEQ ID NO:1164, SEQ ID NO:1170, SEQ ID NO:1172, SEQ ID NO:1175, SEQ ID NO:1182, SEQ ID NO:1184, SEQ ID NO:1208, SEQ ID NO:1210, SEQ ID NO:1212, SEQ ID NO:1214, SEQ ID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1236, SEQ ID NO:1238, SEQ ID NO:1240, SEQ ID NO:1242, SEQ ID NO:1244, SEQ ID NO:1246, SEQ ID NO:1248, SEQ ID NO:1250, SEQ ID NO:1252, SEQ ID NO:1254, SEQ ID NO:1256, SEQ ID NO:1258, SEQ ID NO:1260, SEQ ID NO:1262, SEQ ID NO:1264, SEQ ID NO:1266, SEQ ID NO:1268, SEQ ID NO:1270, SEQ ID NO:1272, SEQ ID NO:1274, SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1282, SEQ ID NO:1284, SEQ ID NO:1291, SEQ ID NO:1293, SEQ ID NO:1295, SEQ ID NO:1297, SEQ ID NO:1299, SEQ ID NO:1301, SEQ ID NO:1310, SEQ ID NO:1312, SEQ ID NO:1314, SEQ ID NO:1316, SEQ ID NO:1318, SEQ ID NO:1320, SEQ ID NO:1322, SEQ ID NO:1324, SEQ ID NO:1326, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1332, SEQ ID NO:1334, SEQ ID NO:1336, SEQ ID NO:1338, SEQ ID NO:1340, SEQ ID NO:1342, SEQ ID NO:1344, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1356, SEQ ID NO:1358, SEQ ID NO:1360, SEQ ID NO:1368, SEQ ID NO:1370, SEQ ID NO:1372, SEQ ID NO:1374, SEQ ID NO:1376, SEQ ID NO:1378, SEQ ID NO:1380, SEQ ID NO:1382, SEQ ID NO:1384, SEQ ID NO:1386, SEQ ID NO:1388, SEQ ID NO:1390, SEQ ID NO:1392, SEQ ID NO:1394, SEQ ID NO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1402, SEQ ID NO:1404, SEQ ID NO:1411, SEQ ID NO:1413, SEQ ID NO:1416, SEQ ID NO:1418, SEQ ID NO:1420, SEQ ID NO:1422, SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1434, SEQ ID NO:1435, SEQ ID NO:1443, SEQ ID NO:1464, SEQ ID NO:1466, SEQ ID NO:1468, SEQ ID NO:1470, SEQ ID NO:1472, SEQ ID NO:1474, SEQ ID NO:1476, SEQ ID NO:1478, SEQ ID NO:1480, SEQ ID NO:1482, SEQ ID NO:1484, SEQ ID NO:1486, SEQ ID NO:1492, SEQ ID NO:1501, SEQ ID NO:1503, SEQ ID NO:1517, SEQ ID NO:1519, SEQ ID NO:1521, SEQ ID NO:1523, SEQ ID NO:1525, SEQ ID NO:1527, SEQ ID NO:1535, SEQ ID NO:1537, SEQ ID NO:1539, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1549, SEQ ID NO:1551, SEQ ID NO:1553, SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1563, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID SEQ ID NO:1569, SEQ ID NO:1572, NO:1574, SEQ ID NO:1576, SEQ ID NO:1578, SEQ ID NO:1580, SEQ ID NO:1582, SEQ ID NO:1584, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1594, SEQ ID NO:1609, SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1619, SEQ ID NO:1623, SEQ ID NO:1625, SEQ ID NO:1627, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1636, SEQ ID NO:1652, SEQ ID NO:1656, SEQ ID NO:1658, SEQ ID NO:1660, SEQ ID NO:1662, SEQ ID NO:1664, SEQ ID NO:1666, SEQ ID NO:1668, SEQ ID NO:1670, SEQ ID NO:1672, SEQ ID NO:1674, SEQ ID NO:1680, SEQ ID NO:1682, SEQ ID NO:1691, SEQ ID NO:1693, SEQ ID NO:1695, SEQ ID NO:1697, SEQ ID NO:1699, SEQ ID NO:1701, SEQ ID NO:1703, SEQ ID NO:1705, SEQ ID NO:1707, SEQ ID NO:1709, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1715, SEQ ID NO:1717, SEQ ID NO:1719, SEQ ID NO:1721, SEQ ID NO:1723, SEQ ID NO:1725, SEQ ID NO:1727, SEQ ID NO:1732, SEQ ID NO:1734, SEQ ID NO:1748, SEQ ID NO:1751, SEQ ID NO:1766, SEQ ID NO:1776, SEQ ID NO:1778, SEQ ID NO:1780, SEQ ID NO:1782, SEQ ID NO:1784, SEQ ID NO:1805, SEQ ID NO:1821, SEQ ID NO:1823, SEQ ID NO:1825, SEQ ID NO:1827, SEQ ID NO:1829, SEQ ID NO:1831, SEQ ID NO:1833, SEQ ID NO:1835, SEQ ID NO:1837, SEQ ID NO:1839, SEQ ID NO:1841, SEQ ID NO:1843, SEQ ID NO:1845, SEQ ID NO:1847, SEQ ID NO:1849, SEQ ID NO:1851, SEQ ID NO:1853, SEQ ID NO:1855, SEQ ID NO:1857, SEQ ID NO:1859, SEQ ID NO:1861, SEQ ID NO:1863, SEQ ID NO:1865, SEQ ID NO:1867, SEQ ID NO:1869, SEQ ID NO:1871, SEQ ID NO:1873, SEQ ID NO:1875, SEQ ID NO:1877, SEQ ID NO:1879, SEQ ID NO:1881, SEQ ID NO:1883, SEQ ID NO:1885, SEQ ID NO:1887, SEQ ID NO:1889, SEQ ID NO:1891, SEQ ID NO:1896, SEQ ID NO:1898, SEQ ID NO:1900, SEQ ID NO:1903, SEQ ID NO:1905, SEQ ID NO:1907, SEQ ID NO:1919, SEQ ID NO:1920, SEQ ID NO:2060, SEQ ID NO:2062, SEQ ID NO:2064, SEQ ID NO:2084, SEQ ID NO:2088, SEQ ID NO:2090, SEQ ID NO:2092, SEQ ID NO:2094, SEQ ID NO:2096, SEQ ID NO:2098, SEQ ID NO:2100, SEQ ID NO:2102, SEQ ID NO:2104, SEQ ID NO:2106, SEQ ID NO:2108, SEQ ID NO:2110, SEQ ID NO:2112, SEQ ID NO:2114, SEQ ID NO:2116, SEQ ID NO:2118, SEQ ID NO:2120, SEQ ID NO:2122, SEQ ID NO:2124, SEQ ID NO:2126, SEQ ID NO:2128, SEQ ID NO:2130, SEQ ID NO:2132, SEQ ID NO:2134, SEQ ID NO:2136, SEQ ID NO:2138, SEQ ID NO:2140, SEQ ID NO:2142, SEQ ID NO:2144, SEQ ID NO:2146, SEQ ID NO:2148, SEQ ID NO:2150, SEQ ID NO:2152, SEQ ID NO:2154, SEQ ID NO:2156, SEQ ID NO:2158, SEQ ID NO:2160, SEQ ID NO:2161, SEQ ID NO:2163, SEQ ID NO:2165, SEQ ID NO:6167, SEQ ID NO:2169, SEQ ID NO:2171, SEQ ID NO:2173, SEQ ID NO:2175, SEQ ID NO:2177, SEQ ID NO:2179, SEQ ID NO:2181, SEQ ID NO:2183, SEQ ID NO:2185, SEQ ID NO:2187, SEQ ID NO:2189, SEQ ID NO:2191, SEQ ID NO:2193, SEQ ID NO:2195, SEQ ID NO:2197, SEQ ID NO:2199, SEQ ID NO:2201, SEQ ID NO:2203, SEQ ID NO:2205, SEQ ID NO:2207, SEQ ID NO:2209, SEQ ID NO:2211, SEQ ID NO:2213, SEQ ID NO:2215, SEQ ID NO:2217, SEQ ID NO:2219, SEQ ID NO:2221, SEQ ID NO:2223, SEQ ID NO:2225, SEQ ID NO:2227, SEQ ID NO:2229, SEQ ID NO:2231, SEQ ID NO:2233, SEQ ID NO:2235, SEQ ID NO:2237, SEQ ID NO:2239, SEQ ID NO:2241, SEQ ID NO:2243, SEQ ID NO:2245, SEQ ID NO:2247, SEQ ID NO:2249, SEQ ID NO:2251, SEQ ID NO:2253, SEQ ID NO:2255, SEQ ID NO:2257, SEQ ID NO:2259, SEQ ID NO:2261, SEQ ID NO:2263, SEQ ID NO:2265, SEQ ID NO:2267, SEQ ID NO:2269, SEQ ID NO:2271, SEQ ID NO:2273, SEQ ID NO:2275, SEQ ID NO:2277, SEQ ID NO:2279, SEQ ID NO:2281, SEQ ID NO:2283, SEQ ID NO:2285, SEQ ID NO:2287, SEQ ID NO:2289, SEQ ID NO:2291, SEQ ID NO:2293, SEQ ID NO:2295, SEQ ID NO:2297, SEQ ID NO:2299, SEQ ID NO:2301, SEQ ID NO:2303, SEQ ID NO:2305, SEQ ID NO:2307, SEQ ID NO:2309, SEQ ID NO:2311, SEQ ID NO:2313, SEQ ID NO:2315, SEQ ID NO:2317, SEQ ID NO:2319, SEQ ID NO:2321, SEQ ID NO:2323, SEQ ID NO:2325, SEQ ID NO:2327, SEQ ID NO:2329, SEQ ID NO:2331, SEQ ID NO:2333, SEQ ID NO:2335, SEQ ID NO:2337, SEQ ID NO:2339, SEQ ID NO:2341, SEQ ID NO:2343, SEQ ID NO:2345, SEQ ID NO:2347, and SEQ ID NO:2349-2690; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

Plant cells comprising an exogenous nucleic acid are provided herein. The exogenous nucleic acid comprises a regulatory region operably linked to a nucleotide sequence encoding a polypeptide. The HMM bit score of the amino acid sequence of the polypeptide is greater than about 20, using an HMM generated from the amino acid sequences depicted in one of FIGS. 1 to 51 or 53 to 131. A tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content of a control plant that does not comprise the nucleic acid. A transgenic plant comprising such a plant cell also is provided.

In another aspect, the plant cell comprises an exogenous nucleic acid comprising a regulatory region operably linked to a polynucleotide encoding a polypeptide comprising an amino acid sequence having 80% or greater sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, SEQ ID NO:2087, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, and SEQ ID NO:2348; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid. A transgenic plant comprising such a plant cell also is provided.

The plant cell can further comprise a sequence of interest operably linked to a regulatory region associated with the polypeptide. The sequence of interest can inhibit expression of an endogenous gene involved in lignin biosynthesis. The sequence of interest can be in antisense orientation relative to the regulatory region. The sequence of interest can be transcribed into an interfering RNA. The endogenous gene can comprise a coding sequence for a regulatory protein involved in lignin biosynthesis. The endogenous gene can comprise a coding sequence for a lignin biosynthesis enzyme. The enzyme can be 4-(hydroxy)cinnamoyl CoA ligase (4CL; EC 6.2.1.12), p-coumarate 3-hydroxylase (C3H), cinnamate 4-hydroxylase (C4H; EC 1.14.13.11), cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195), caffeoyl CoA O-methyltransferase (CCoAOMT; EC 2.1.1.104), cinnamoyl CoA reductase (CCR; EC 1.2.1.44), caffeic acid/5-hydroxyferulic acid O-methyltransferase (COMT; EC 2.1.1.68), hydroxycinnamoyl CoA:quinate hydroxycinnamoyltransferase (CQT; EC 2.3.1.99), hydroxycinnamoyl CoA:shikimate hydroxycinnamoyltransferase (CST; EC 2.3.1.133), ferulate 5-hydroxylase (F5H), phenylalanine ammonia-lyase (PAL; EC 4.3.1.5), p-coumaryl CoA 3-hydroxylase (pCCoA3H), sinapyl alcohol dehydrogenase (SAD), a peroxidase enzyme (EC 1.11.1.x), laccase (EC 1.10.3.2), coniferyl-alcohol glucosyltransferase (EC 2.4.1.111), or coniferin β-glucosidase (EC 3.2.1.126). The regulatory region and its associated polypeptide can be effective for increasing lignin biosynthesis. The regulatory region and its associated polypeptide can be effective for decreasing lignin biosynthesis.

The polypeptide can modulate the expression of an endogenous gene involved in lignin biosynthesis. The endogenous gene can comprise a coding sequence for a lignin biosynthesis enzyme. The endogenous gene can comprise a coding sequence for a regulatory protein involved in lignin biosynthesis. The modulation of the endogenous gene can be an increase in expression of the endogenous gene.

The plant cell can further comprise a nucleic acid encoding a second polypeptide operably linked to a regulatory region, where the second polypeptide encodes a regulatory protein. The nucleic acid can be on a second recombinant nucleic acid construct.

In another aspect, the plant cell comprises an exogenous nucleic acid comprising a regulatory region operably linked to a nucleic acid sequence having 95% or greater sequence identity to an nucleic acid sequence selected from the group consisting of SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:118, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:129, SEQ ID NO:133, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:148, SEQ ID NO:150, SEQ ID NO:156, SEQ ID NO:158, SEQ ID NO:160, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:169, SEQ ID NO:171, SEQ ID NO:177, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:271, SEQ ID NO:274, SEQ ID NO:278, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:314, SEQ ID NO:317, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:327, SEQ ID NO:329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:336, SEQ ID NO:338, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:352, SEQ ID NO:354, SEQ ID NO:356, SEQ ID NO:360, SEQ ID NO:369, SEQ ID NO:371, SEQ ID NO:373, SEQ ID NO:376, SEQ ID NO:378, SEQ ID NO:380, SEQ ID NO:386, SEQ ID NO:390, SEQ ID NO:393, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID NO:416, SEQ ID NO:431, SEQ ID NO:435, SEQ ID NO:437, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:444, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:453, SEQ ID NO:458, SEQ ID NO:460, SEQ ID NO:464, SEQ ID NO:469, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:477, SEQ ID NO:482, SEQ ID NO:486, SEQ ID NO:489, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:500, SEQ ID NO:503, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:515, SEQ ID NO:517, SEQ ID NO:519, SEQ ID NO:523, SEQ ID NO:525, SEQ ID NO:528, SEQ ID NO:534, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:544, SEQ ID NO:547, SEQ ID NO:552, SEQ ID NO:554, SEQ ID NO:562, SEQ ID NO:565, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:573, SEQ ID NO:577, SEQ ID NO:580, SEQ ID NO:582, SEQ ID NO:584, SEQ ID NO:589, SEQ ID NO:592, SEQ ID NO:595, SEQ ID NO:598, SEQ ID NO:600, SEQ ID NO:602, SEQ ID NO:605, SEQ ID NO:607, SEQ ID NO:609, SEQ ID NO:611, SEQ ID NO:613, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:637, SEQ ID NO:649, SEQ ID NO:651, SEQ ID NO:655, SEQ ID NO:658, SEQ ID NO:660, SEQ ID NO:664, SEQ ID NO:670, SEQ ID NO:674, SEQ ID NO:677, SEQ ID NO:679, SEQ ID NO:681, SEQ ID NO:683, SEQ ID NO:685, SEQ ID NO:688, SEQ ID NO:694, SEQ ID NO:697, SEQ ID NO:699, SEQ ID NO:702, SEQ ID NO:704, SEQ ID NO:706, SEQ ID NO:708, SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:717, SEQ ID NO:719, SEQ ID NO:721, SEQ ID NO:723, SEQ ID NO:729, SEQ ID NO:736, SEQ ID NO:741, SEQ ID NO:743, SEQ ID NO:746, SEQ ID NO:752, SEQ ID NO:754, SEQ ID NO:759, SEQ ID NO:764, SEQ ID NO:778, SEQ ID NO:780, SEQ ID NO:785, SEQ ID NO:789, SEQ ID NO:792, SEQ ID NO:795, SEQ ID NO:797, SEQ ID NO:799, SEQ ID NO:801, SEQ ID NO:807, SEQ ID NO:810, SEQ ID NO:813, SEQ ID NO:815, SEQ ID NO:819, SEQ ID NO:821, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:829, SEQ ID NO:832, SEQ ID NO:834, SEQ ID NO:837, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:848, SEQ ID NO:851, SEQ ID NO:854, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:864, SEQ ID NO:867, SEQ ID NO:884, SEQ ID NO:889, SEQ ID NO:891, SEQ ID NO:893, SEQ ID NO:895, SEQ ID NO:897, SEQ ID NO:899, SEQ ID NO:903, SEQ ID NO:906, SEQ ID NO:911, SEQ ID NO:913, SEQ ID NO:916, SEQ ID NO:918, SEQ ID NO:920, SEQ ID NO:926, SEQ ID NO:928, SEQ ID NO:933, SEQ ID NO:935, SEQ ID NO:937, SEQ ID NO:942, SEQ ID NO:944, SEQ ID NO:958, SEQ ID NO:963, SEQ ID NO:965, SEQ ID NO:967, SEQ ID NO:972, SEQ ID NO:974, SEQ ID NO:979, SEQ ID NO:981, SEQ ID NO:993, SEQ ID NO:1006, SEQ ID NO:1010, SEQ ID NO:1015, SEQ ID NO:1027, SEQ ID NO:1030, SEQ ID NO:1034, SEQ ID NO:1049, SEQ ID NO:1051, SEQ ID NO:1054, SEQ ID NO:1057, SEQ ID NO:1059, SEQ ID NO:1061, SEQ ID NO:1063, SEQ ID NO:1067, SEQ ID NO:1070, SEQ ID NO:1077, SEQ ID NO:1080, SEQ ID NO:1082, SEQ ID NO:1084, SEQ ID NO:1086, SEQ ID NO:1090, SEQ ID NO:1093, SEQ ID NO:1095, SEQ ID NO:1097, SEQ ID NO:1103, SEQ ID NO:1108, SEQ ID NO:1116, SEQ ID NO:1121, SEQ ID NO:1124, SEQ ID NO:1128, SEQ ID NO:1130, SEQ ID NO:1133, SEQ ID NO:1135, SEQ ID NO:1138, SEQ ID NO:1142, SEQ ID NO:1148, SEQ ID NO:1155, SEQ ID NO:1158, SEQ ID NO:1160, SEQ ID NO:1162, SEQ ID NO:1164, SEQ ID NO:1170, SEQ ID NO:1172, SEQ ID NO:1175, SEQ ID NO:1182, SEQ ID NO:1184, SEQ ID NO:1208, SEQ ID NO:1210, SEQ ID NO:1212, SEQ ID NO:1214, SEQ ID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1236, SEQ ID NO:1238, SEQ ID NO:1240, SEQ ID NO:1242, SEQ ID NO:1244, SEQ ID NO:1246, SEQ ID NO:1248, SEQ ID NO:1250, SEQ ID NO:1252, SEQ ID NO:1254, SEQ ID NO:1256, SEQ ID NO:1258, SEQ ID NO:1260, SEQ ID NO:1262, SEQ ID NO:1264, SEQ ID NO:1266, SEQ ID NO:1268, SEQ ID NO:1270, SEQ ID NO:1272, SEQ ID NO:1274, SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1282, SEQ ID NO:1284, SEQ ID NO:1291, SEQ ID NO:1293, SEQ ID NO:1295, SEQ ID NO:1297, SEQ ID NO:1299, SEQ ID NO:1301, SEQ ID NO:1310, SEQ ID NO:1312, SEQ ID NO:1314, SEQ ID NO:1316, SEQ ID NO:1318, SEQ ID NO:1320, SEQ ID NO:1322, SEQ ID NO:1324, SEQ ID NO:1326, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1332, SEQ ID NO:1334, SEQ ID NO:1336, SEQ ID NO:1338, SEQ ID NO:1340, SEQ ID NO:1342, SEQ ID NO:1344, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1356, SEQ ID NO:1358, SEQ ID NO:1360, SEQ ID NO:1368, SEQ ID NO:1370, SEQ ID NO:1372, SEQ ID NO:1374, SEQ ID NO:1376, SEQ ID NO:1378, SEQ ID NO:1380, SEQ ID NO:1382, SEQ ID NO:1384, SEQ ID NO:1386, SEQ ID NO:1388, SEQ ID NO:1390, SEQ ID NO:1392, SEQ ID NO:1394, SEQ ID NO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1402, SEQ ID NO:1404, SEQ ID NO:1411, SEQ ID NO:1413, SEQ ID NO:1416, SEQ ID NO:1418, SEQ ID NO:1420, SEQ ID NO:1422, SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1434, SEQ ID NO:1435, SEQ ID NO:1443, SEQ ID NO:1464, SEQ ID NO:1466, SEQ ID NO:1468, SEQ ID NO:1470, SEQ ID NO:1472, SEQ ID NO:1474, SEQ ID NO:1476, SEQ ID NO:1478, SEQ ID NO:1480, SEQ ID NO:1482, SEQ ID NO:1484, SEQ ID NO:1486, SEQ ID NO:1492, SEQ ID NO:1501, SEQ ID NO:1503, SEQ ID NO:1517, SEQ ID NO:1519, SEQ ID NO:1521, SEQ ID NO:1523, SEQ ID NO:1525, SEQ ID NO:1527, SEQ ID NO:1535, SEQ ID NO:1537, SEQ ID NO:1539, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1549, SEQ ID NO:1551, SEQ ID NO:1553, SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1563, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID SEQ ID NO:1569, SEQ ID NO:1572, NO:1574, SEQ ID NO:1576, SEQ ID NO:1578, SEQ ID NO:1580, SEQ ID NO:1582, SEQ ID NO:1584, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1594, SEQ ID NO:1609, SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1619, SEQ ID NO:1623, SEQ ID NO:1625, SEQ ID NO:1627, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1636, SEQ ID NO:1652, SEQ ID NO:1656, SEQ ID NO:1658, SEQ ID NO:1660, SEQ ID NO:1662, SEQ ID NO:1664, SEQ ID NO:1666, SEQ ID NO:1668, SEQ ID NO:1670, SEQ ID NO:1672, SEQ ID NO:1674, SEQ ID NO:1680, SEQ ID NO:1682, SEQ ID NO:1691, SEQ ID NO:1693, SEQ ID NO:1695, SEQ ID NO:1697, SEQ ID NO:1699, SEQ ID NO:1701, SEQ ID NO:1703, SEQ ID NO:1705, SEQ ID NO:1707, SEQ ID NO:1709, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1715, SEQ ID NO:1717, SEQ ID NO:1719, SEQ ID NO:1721, SEQ ID NO:1723, SEQ ID NO:1725, SEQ ID NO:1727, SEQ ID NO:1732, SEQ ID NO:1734, SEQ ID NO:1748, SEQ ID NO:1751, SEQ ID NO:1766, SEQ ID NO:1776, SEQ ID NO:1778, SEQ ID NO:1780, SEQ ID NO:1782, SEQ ID NO:1784, SEQ ID NO:1805, SEQ ID NO:1821, SEQ ID NO:1823, SEQ ID NO:1825, SEQ ID NO:1827, SEQ ID NO:1829, SEQ ID NO:1831, SEQ ID NO:1833, SEQ ID NO:1835, SEQ ID NO:1837, SEQ ID NO:1839, SEQ ID NO:1841, SEQ ID NO:1843, SEQ ID NO:1845, SEQ ID NO:1847, SEQ ID NO:1849, SEQ ID NO:1851, SEQ ID NO:1853, SEQ ID NO:1855, SEQ ID NO:1857, SEQ ID NO:1859, SEQ ID NO:1861, SEQ ID NO:1863, SEQ ID NO:1865, SEQ ID NO:1867, SEQ ID NO:1869, SEQ ID NO:1871, SEQ ID NO:1873, SEQ ID NO:1875, SEQ ID NO:1877, SEQ ID NO:1879, SEQ ID NO:1881, SEQ ID NO:1883, SEQ ID NO:1885, SEQ ID NO:1887, SEQ ID NO:1889, SEQ ID NO:1891, SEQ ID NO:1896, SEQ ID NO:1898, SEQ ID NO:1900, SEQ ID NO:1903, SEQ ID NO:1905, SEQ ID NO:1907, SEQ ID NO:1919, SEQ ID NO:1920, SEQ ID NO:2060, SEQ ID NO:2062, SEQ ID NO:2064, SEQ ID NO:2084, SEQ ID NO:2088, SEQ ID NO:2090, SEQ ID NO:2092, SEQ ID NO:2094, SEQ ID NO:2096, SEQ ID NO:2098, SEQ ID NO:2100, SEQ ID NO:2102, SEQ ID NO:2104, SEQ ID NO:2106, SEQ ID NO:2108, SEQ ID NO:2110, SEQ ID NO:2112, SEQ ID NO:2114, SEQ ID NO:2116, SEQ ID NO:2118, SEQ ID NO:2120, SEQ ID NO:2122, SEQ ID NO:2124, SEQ ID NO:2126, SEQ ID NO:2128, SEQ ID NO:2130, SEQ ID NO:2132, SEQ ID NO:2134, SEQ ID NO:2136, SEQ ID NO:2138, SEQ ID NO:2140, SEQ ID NO:2142, SEQ ID NO:2144, SEQ ID NO:2146, SEQ ID NO:2148, SEQ ID NO:2150, SEQ ID NO:2152, SEQ ID NO:2154, SEQ ID NO:2156, SEQ ID NO:2158, SEQ ID NO:2160, SEQ ID NO:2161, SEQ ID NO:2163, SEQ ID NO:2165, SEQ ID NO:6167, SEQ ID NO:2169, SEQ ID NO:2171, SEQ ID NO:2173, SEQ ID NO:2175, SEQ ID NO:2177, SEQ ID NO:2179, SEQ ID NO:2181, SEQ ID NO:2183, SEQ ID NO:2185, SEQ ID NO:2187, SEQ ID NO:2189, SEQ ID NO:2191, SEQ ID NO:2193, SEQ ID NO:2195, SEQ ID NO:2197, SEQ ID NO:2199, SEQ ID NO:2201, SEQ ID NO:2203, SEQ ID NO:2205, SEQ ID NO:2207, SEQ ID NO:2209, SEQ ID NO:2211, SEQ ID NO:2213, SEQ ID NO:2215, SEQ ID NO:2217, SEQ ID NO:2219, SEQ ID NO:2221, SEQ ID NO:2223, SEQ ID NO:2225, SEQ ID NO:2227, SEQ ID NO:2229, SEQ ID NO:2231, SEQ ID NO:2233, SEQ ID NO:2235, SEQ ID NO:2237, SEQ ID NO:2239, SEQ ID NO:2241, SEQ ID NO:2243, SEQ ID NO:2245, SEQ ID NO:2247, SEQ ID NO:2249, SEQ ID NO:2251, SEQ ID NO:2253, SEQ ID NO:2255, SEQ ID NO:2257, SEQ ID NO:2259, SEQ ID NO:2261, SEQ ID NO:2263, SEQ ID NO:2265, SEQ ID NO:2267, SEQ ID NO:2269, SEQ ID NO:2271, SEQ ID NO:2273, SEQ ID NO:2275, SEQ ID NO:2277, SEQ ID NO:2279, SEQ ID NO:2281, SEQ ID NO:2283, SEQ ID NO:2285, SEQ ID NO:2287, SEQ ID NO:2289, SEQ ID NO:2291, SEQ ID NO:2293, SEQ ID NO:2295, SEQ ID NO:2297, SEQ ID NO:2299, SEQ ID NO:2301, SEQ ID NO:2303, SEQ ID NO:2305, SEQ ID NO:2307, SEQ ID NO:2309, SEQ ID NO:2311, SEQ ID NO:2313, SEQ ID NO:2315, SEQ ID NO:2317, SEQ ID NO:2319, SEQ ID NO:2321, SEQ ID NO:2323, SEQ ID NO:2325, SEQ ID NO:2327, SEQ ID NO:2329, SEQ ID NO:2331, SEQ ID NO:2333, SEQ ID NO:2335, SEQ ID NO:2337, SEQ ID NO:2339, SEQ ID NO:2341, SEQ ID NO:2343, SEQ ID NO:2345, SEQ ID NO:2347, and SEQ ID NO:2349-2690; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid. A transgenic plant comprising such a plant cell also is provided.

The plant cell can be capable of producing one or more lignin monomers. The plant cell can be from a genus selected from the group consisting of Acer, Aesculus, Afzelia, Agrostis, Alnus, Avena, Cannabis, Carya, Cinnamomum, Coffea, Eucalyptus, Festuca, Fraxinus, Hordeum, Juglans, Lolium, Medicago, Milium, Miscanthus, Panicum, Pinus, Poa, Populus, Prunus, Quercus, Saccharum, Simarouba, Sorghum, Trifolium, Triticum, Vitis, and Zea. The plant cell can be from a species selected from Miscanthus hybrid (Miscanthus×giganteus), Miscanthus sinensis, Miscanthus sacchariflorus, Panicum virgatum, Populus trichocarpa.

The regulatory region can be involved in lignin or cellulose biosynthesis. The regulatory region can be selected from the group consisting of SEQ ID NOs:1909-1918. The regulatory region can be unassociated with the polypeptide. The regulatory region can be a promoter. The promoter can be a tissue-preferential promoter. The tissue can be vascular, stem, pith, xylem, phloem, fruit, seed, seed pod, root, tuber, inflorescence, or leaf tissue. The promoter can be a cell-type preferential promoter. The cell can be a sieve cell, a laticifer cell, a sclerenchyma cell, a xylem cell, or trichome cell. The promoter can be inducible.

In another aspect, forage comprising tissue from the transgenic plant is provided.

A method of expressing a sequence of interest is provided herein. The method comprises growing a plant cell comprising an exogenous nucleic acid comprising a regulatory region operably linked to a sequence of interest and an exogenous nucleic acid comprising a nucleic acid encoding a polypeptide, where the regulatory region and the polypeptide are associated, and where the plant cell expresses the sequence of interest. The polypeptide has 80% or greater sequence identity to SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, SEQ ID NO:2087, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, and SEQ ID NO:2348. The plant cell is grown under conditions effective for expression of the regulatory protein.

In another aspect, the method comprises growing a plant cell comprising an exogenous nucleic acid encoding the sequence of interest operably linked to a regulatory region. The regulatory region comprises a nucleic acid having 80% or greater sequence identity to a regulatory region selected from the group consisting of SEQ ID NOs:1909-1918. The plant cell is grown under conditions effective for expression of the regulatory protein. The regulatory region and the polypeptide are associated and the plant cell expresses the sequence of interest.

The exogenous nucleic acid comprising the regulatory region operably linked to the sequence of interest and the exogenous nucleic acid comprising the nucleic acid encoding the polypeptide can be included in the same nucleic acid construct or separate nucleic acid constructs.

The sequence of interest can comprise a coding sequence for a polypeptide involved in lignin biosynthesis. The sequence of interest can be in antisense orientation. The sequence of interest can be transcribed into an interfering RNA.

In another aspect, a method of expressing a sequence of interest in a plant cell is provided. The method comprises growing a plant cell comprising an exogenous nucleic acid encoding a polypeptide sequence having 80% or greater sequence identity to a polypeptide sequence selected from the group consisting of SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, SEQ ID NO:2087, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, and SEQ ID NO:2348. The plant cell has an endogenous gene involved in lignin biosynthesis comprising a regulatory region and the sequence of interest. The endogenous regulatory region and the polypeptide are associated. The plant cell is grown under conditions effective for expression of the polypeptide and expresses the sequence of interest.

The sequence of interest can comprise a coding sequence for a polypeptide involved in lignin biosynthesis. The endogenous gene can comprise a coding sequence for a polypeptide involved in lignin biosynthesis. The exogenous nucleic acid encoding the polypeptide can be operably linked to a regulatory region capable of modulating expression of the polypeptide in the cell. The regulatory region can be tissue-preferential, cell-type preferential, organ-preferential, or inducible.

In another aspect, a plant is provided. The plant comprises any of the plant cells described above. Progeny of the plant also are provided, where the progeny have a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

Methods of modulating the level of lignin in a plant are provided herein. In one aspect, a method comprises introducing into a plant cell an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide, wherein the HMM bit score of the amino acid sequence of said polypeptide is greater than about 20, said HMM based on the amino acid sequences depicted in one of FIGS. 1 to 51 or 53 to 131, and wherein a tissue of a plant produced from said plant cell has a difference in the lignin content as compared to the corresponding lignin content of a control plant that does not comprise said exogenous nucleic acid.

In another aspect, a method of modulating the lignin content in a plant is provided. The method comprises introducing into a plant cell an exogenous nucleic acid comprising a regulatory region operably linked to a nucleic acid encoding a lignin-modulating polypeptide comprising a polypeptide sequence having 80% or greater sequence identity to a polypeptide sequence selected from the group consisting of SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, SEQ ID NO:2087, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, and SEQ ID NO:2348; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

In another aspect, a method of modulating the lignin content in a plant is provided. The method comprises introducing into a plant cell an exogenous nucleic acid comprising a regulatory region operably linked to a polynucleotide whose transcription product is at least 30 nucleotides in length and is complementary to a nucleic acid encoding a lignin-modulating polypeptide, the lignin-modulating polypeptide selected from the group consisting of a polypeptide having 80% or greater sequence identity to SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, SEQ ID NO:2087, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, and SEQ ID NO:2348; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

In another aspect, a plant cell is provided. The plant cell comprises an exogenous nucleic acid comprising a regulatory region operably linked to a polynucleotide that is transcribed into an interfering RNA effective for inhibiting expression of a lignin-modulating polypeptide selected from the group consisting of a polypeptide having 80% or greater sequence identity to SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, SEQ ID NO:2087, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, and SEQ ID NO:2348; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

The exogenous nucleic acid can further comprise a 3′ UTR operably linked to the polynucleotide. The polynucleotide can be transcribed into an interfering RNA comprising a stem-loop structure. The stem-loop structure can comprise an inverted repeat of the 3′ UTR. The difference can be a decreased lignin content.

In another aspect, an isolated nucleic acid molecule is provided. The isolated nucleic acid molecule comprises a nucleotide sequence having 95% or greater sequence identity to the nucleotide sequence set forth in SEQ ID NO:97, SEQ ID NO:101, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:129, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:150, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:271, SEQ ID NO:274, SEQ ID NO:278, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:314, SEQ ID NO:317, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:327, 329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:352, SEQ ID NO:376, SEQ ID NO:386, SEQ ID NO:390, SEQ ID NO:393, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:453, SEQ ID NO:458, SEQ ID NO:469, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:477, SEQ ID NO:482, SEQ ID NO:486, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:500, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:515, SEQ ID NO:534, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:544, SEQ ID NO:552, SEQ ID NO:562, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:573, SEQ ID NO:577, SEQ ID NO:580, SEQ ID NO:592, SEQ ID NO:595, SEQ ID NO:602, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:649, SEQ ID NO:655, SEQ ID NO:658, SEQ ID NO:664, SEQ ID NO:674, SEQ ID NO:681, SEQ ID NO:683, SEQ ID NO:699, SEQ ID NO:704, SEQ ID NO:708, SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:717, SEQ ID NO:719, SEQ ID NO:721, SEQ ID NO:723, SEQ ID NO:746, SEQ ID NO:752, SEQ ID NO:754, SEQ ID NO:764, SEQ ID NO:785, SEQ ID NO:789, SEQ ID NO:795, SEQ ID NO:797, SEQ ID NO:799, SEQ ID NO:801, SEQ ID NO:810, SEQ ID NO:819, SEQ ID NO:821, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:829, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:848, SEQ ID NO:854, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:867, SEQ ID NO:889, SEQ ID NO:891, SEQ ID NO:893, SEQ ID NO:895, SEQ ID NO:903, SEQ ID NO:906, SEQ ID NO:911, SEQ ID NO:916, SEQ ID NO:918, SEQ ID NO:920, SEQ ID NO:926, SEQ ID NO:928, SEQ ID NO:942, SEQ ID NO:944, SEQ ID NO:958, SEQ ID NO:965, SEQ ID NO:967, SEQ ID NO:972, SEQ ID NO:974, SEQ ID NO:981, SEQ ID NO:1006, SEQ ID NO:1010, SEQ ID NO:1015, SEQ ID NO:1027, SEQ ID NO:1030, SEQ ID NO:1034, SEQ ID NO:1054, SEQ ID NO:1067, SEQ ID NO:1070, SEQ ID NO:1077, SEQ ID NO:1084, SEQ ID NO:1086, SEQ ID NO:1090, SEQ ID NO:1093, SEQ ID NO:1097, SEQ ID NO:1108, SEQ ID NO:1116, SEQ ID NO:1121, SEQ ID NO:1124, SEQ ID NO:1138, SEQ ID NO:1142, SEQ ID NO:1148, SEQ ID NO:1155, SEQ ID NO:1158, SEQ ID NO:1160, SEQ ID NO:1170, SEQ ID NO:1172, SEQ ID NO:1175, SEQ ID NO:1208, SEQ ID NO:1212, SEQ ID NO:1214, SEQ ID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1236, SEQ ID NO:1240, SEQ ID NO:1242, SEQ ID NO:1244, SEQ ID NO:1246, SEQ ID NO:1250, SEQ ID NO:1252, SEQ ID NO:1254, SEQ ID NO:1256, SEQ ID NO:1260, SEQ ID NO:1262, SEQ ID NO:1264, SEQ ID NO:1268, SEQ ID NO:1270, SEQ ID NO:1272, SEQ ID NO:1274, SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1282, SEQ ID NO:1291, SEQ ID NO:1295, SEQ ID NO:1297, SEQ ID NO:1299, SEQ ID NO:1310, SEQ ID NO:1312, SEQ ID NO:1316, SEQ ID NO:1318, SEQ ID NO:1320, SEQ ID NO:1324, SEQ ID NO:1326, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1334, SEQ ID NO:1336, SEQ ID NO:1338, SEQ ID NO:1340, SEQ ID NO:1342, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1356, SEQ ID NO:1358, SEQ ID NO:1368, SEQ ID NO:1372, SEQ ID NO:1374, SEQ ID NO:1378, SEQ ID NO:1380, SEQ ID NO:1384, SEQ ID NO:1386, SEQ ID NO:1388, SEQ ID NO:1390, NO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1402, SEQ ID NO:1411, SEQ ID NO:1416, SEQ ID NO:1418, SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1466, SEQ ID NO:1470, SEQ ID NO:1476, SEQ ID NO:1478, SEQ ID NO:1482, SEQ ID NO:1484, SEQ ID NO:1486, SEQ ID NO:1501, SEQ ID NO:1519, SEQ ID NO:1521, SEQ ID NO:1523, SEQ ID NO:1527, SEQ ID NO:1535, SEQ ID NO:1537, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1549, SEQ ID NO:1553, SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID NO:1574, SEQ ID NO:1576, SEQ ID NO:1578, SEQ ID NO:1582, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1623, SEQ ID NO:1625, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1656, SEQ ID NO:1658, SEQ ID NO:1662, SEQ ID NO:1664, SEQ ID NO:1666, SEQ ID NO:1668, SEQ ID NO:1670, SEQ ID NO:1672, SEQ ID NO:1682, SEQ ID NO:1693, SEQ ID NO:1695, SEQ ID NO:1699, SEQ ID NO:1701, SEQ ID NO:1703, SEQ ID NO:1705, SEQ ID NO:1707, SEQ ID NO:1709, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1715, SEQ ID NO:1717, SEQ ID NO:1719, SEQ ID NO:1723, SEQ ID NO:1725, SEQ ID NO:1732, SEQ ID NO:1748, SEQ ID NO:1776, SEQ ID NO:1780, SEQ ID NO:1782, SEQ ID NO:1833, SEQ ID NO:1855, SEQ ID NO:1891, SEQ ID NO:1898, SEQ ID NO:1900, SEQ ID NO:1907, SEQ ID NO:2060, SEQ ID NO:2062, SEQ ID NO:2064, SEQ ID NO:2088, SEQ ID NO:2090, SEQ ID NO:2092, SEQ ID NO:2094, SEQ ID NO:2096, SEQ ID NO:2098, SEQ ID NO:2100, SEQ ID NO:2102, SEQ ID NO:2104, SEQ ID NO:2106, SEQ ID NO:2108, SEQ ID NO:2110, SEQ ID NO:2112, SEQ ID NO:2114, SEQ ID NO:2116, SEQ ID NO:2118, SEQ ID NO:2120, SEQ ID NO:2122, SEQ ID NO:2124, SEQ ID NO:2126, SEQ ID NO:2128, SEQ ID NO:2130, SEQ ID NO:2132, SEQ ID NO:2134, SEQ ID NO:2136, SEQ ID NO:2138, SEQ ID NO:2140, SEQ ID NO:2142, SEQ ID NO:2144, SEQ ID NO:2146, SEQ ID NO:2148, SEQ ID NO:2150, SEQ ID NO:2152, SEQ ID NO:2154, SEQ ID NO:2156, SEQ ID NO:2158, SEQ ID NO:2160, SEQ ID NO:2161, SEQ ID NO:2163, SEQ ID NO:2165, SEQ ID NO:6167, SEQ ID NO:2169, SEQ ID NO:2171, SEQ ID NO:2173, SEQ ID NO:2175, SEQ ID NO:2177, SEQ ID NO:2179, SEQ ID NO:2181, SEQ ID NO:2183, SEQ ID NO:2185, SEQ ID NO:2187, SEQ ID NO:2189, SEQ ID NO:2191, SEQ ID NO:2193, SEQ ID NO:2195, SEQ ID NO:2197, SEQ ID NO:2199, SEQ ID NO:2201, SEQ ID NO:2203, SEQ ID NO:2205, SEQ ID NO:2207, SEQ ID NO:2209, SEQ ID NO:2211, SEQ ID NO:2213, SEQ ID NO:2215, SEQ ID NO:2217, SEQ ID NO:2219, SEQ ID NO:2221, SEQ ID NO:2223, SEQ ID NO:2225, SEQ ID NO:2227, SEQ ID NO:2229, SEQ ID NO:2231, SEQ ID NO:2233, SEQ ID NO:2235, SEQ ID NO:2237, SEQ ID NO:2239, SEQ ID NO:2241, SEQ ID NO:2243, SEQ ID NO:2245, SEQ ID NO:2247, SEQ ID NO:2249, SEQ ID NO:2251, SEQ ID NO:2253, SEQ ID NO:2255, SEQ ID NO:2257, SEQ ID NO:2259, SEQ ID NO:2261, SEQ ID NO:2263, SEQ ID NO:2265, SEQ ID NO:2267, SEQ ID NO:2269, SEQ ID NO:2271, SEQ ID NO:2273, SEQ ID NO:2275, SEQ ID NO:2277, SEQ ID NO:2279, SEQ ID NO:2281, SEQ ID NO:2283, SEQ ID NO:2285, SEQ ID NO:2287, SEQ ID NO:2289, SEQ ID NO:2291, SEQ ID NO:2293, SEQ ID NO:2295, SEQ ID NO:2297, SEQ ID NO:2299, SEQ ID NO:2301, SEQ ID NO:2303, SEQ ID NO:2305, SEQ ID NO:2307, SEQ ID NO:2309, SEQ ID NO:2311, SEQ ID NO:2313, SEQ ID NO:2315, SEQ ID NO:2317, SEQ ID NO:2319, SEQ ID NO:2321, SEQ ID NO:2323, SEQ ID NO:2325, SEQ ID NO:2327, SEQ ID NO:2329, SEQ ID NO:2331, SEQ ID NO:2333, SEQ ID NO:2335, SEQ ID NO:2337, SEQ ID NO:2339, SEQ ID NO:2341, SEQ ID NO:2343, SEQ ID NO:2345, SEQ ID NO:2347, or SEQ ID NO:2690.

In another aspect, an isolated nucleic acid is provided. The isolated nucleic acid comprises a nucleotide sequence encoding a polypeptide having 80% or greater sequence identity to the amino acid sequence set forth in SEQ ID NO:98, SEQ ID NO:102, SEQ ID NO:108, SEQ ID NO:110, SEQ ID NO:114, SEQ ID NO:124, SEQ ID NO:126, SEQ ID NO:130, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:151, SEQ ID NO:196, SEQ ID NO:198, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NO:253, SEQ ID NO:255, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NO:262, SEQ ID NO:267, SEQ ID NO:269, SEQ ID NO:272, SEQ ID NO:275, SEQ ID NO:279, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NO:286, SEQ ID NO:289, SEQ ID NO:292, SEQ ID NO:294, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NO:308, SEQ ID NO:315, SEQ ID NO:318, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NO:325, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NO:334, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347, SEQ ID NO:353, SEQ ID NO:377, SEQ ID NO:387, SEQ ID NO:391, SEQ ID NO:394, SEQ ID NO:400, SEQ ID NO:402, SEQ ID NO:440, SEQ ID NO:442, SEQ ID NO:449, SEQ ID NO:451, SEQ ID NO:454, SEQ ID NO:459, SEQ ID NO:470, SEQ ID NO:473, SEQ ID NO:475, SEQ ID NO:478, SEQ ID NO:483, SEQ ID NO:487, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NO:496, SEQ ID NO:501, SEQ ID NO:508, SEQ ID NO:510, SEQ ID NO:516, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NO:545, SEQ ID NO:553, SEQ ID NO:563, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NO:574, SEQ ID NO:578, SEQ ID NO:581, SEQ ID NO:593, SEQ ID NO:596, SEQ ID NO:603, SEQ ID NO:619, SEQ ID NO:621, SEQ ID NO:650, SEQ ID NO:656, SEQ ID NO:659, SEQ ID NO:665, SEQ ID NO:675, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NO:700, SEQ ID NO:705, SEQ ID NO:709, SEQ ID NO:713, SEQ ID NO:715, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NO:724, SEQ ID NO:747, SEQ ID NO:753, SEQ ID NO:755, SEQ ID NO:765, SEQ ID NO:786, SEQ ID NO:780, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NO:802, SEQ ID NO:811, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:830, SEQ ID NO:841, SEQ ID NO:843, SEQ ID NO:849, SEQ ID NO:855, SEQ ID NO:859, SEQ ID NO:861, SEQ ID NO:868, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:904, SEQ ID NO:907, SEQ ID NO:912, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NO:921, SEQ ID NO:927, SEQ ID NO:929, SEQ ID NO:943, SEQ ID NO:945, SEQ ID NO:959, SEQ ID NO:966, SEQ ID NO:968, SEQ ID NO:973, SEQ ID NO:975, SEQ ID NO:982, SEQ ID NO:1007, SEQ ID NO:1011, SEQ ID NO:1016, SEQ ID NO:1028, SEQ ID NO:1031, SEQ ID NO:1035, SEQ ID NO:1055, SEQ ID NO:1068, SEQ ID NO:1071, SEQ ID NO:1078, SEQ ID NO:1085, SEQ ID NO:1087, SEQ ID NO:1091, SEQ ID NO:1094, SEQ ID NO:1098, SEQ ID NO:1109, SEQ ID NO:1117, SEQ ID NO:1122, SEQ ID NO:1125, SEQ ID NO:1139, SEQ ID NO:1143, SEQ ID NO:1149, SEQ ID NO:1156, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1171, SEQ ID NO:1173, SEQ ID NO:1176, SEQ ID NO:1209, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NO:1225, SEQ ID NO:1237, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NO:1292, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NO:1369, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NO:1412, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NO:1467, SEQ ID NO:1471, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NO:1487, SEQ ID NO:1502, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1528, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1583, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1630, SEQ ID NO:1632, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NO:1683, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710, SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NO:1733, SEQ ID NO:1749, SEQ ID NO:1777, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NO:1834, SEQ ID NO:1856, SEQ ID NO:1892, SEQ ID NO:1899, SEQ ID NO:1901, SEQ ID NO:1908, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NO:2065, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, SEQ ID NO:2348, or SEQ ID NO:1747.

In another aspect, an isolated nucleic acid is provided. The isolated nucleic acid comprises a nucleotide sequence having 95% or greater sequence identity to the nucleic acid sequence set forth in SEQ ID NO:97, SEQ ID NO:101, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:129, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:150, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:271, SEQ ID NO:274, SEQ ID NO:278, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:314, SEQ ID NO:317, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:327, 329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:352, SEQ ID NO:376, SEQ ID NO:386, SEQ ID NO:390, SEQ ID NO:393, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:453, SEQ ID NO:458, SEQ ID NO:469, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:477, SEQ ID NO:482, SEQ ID NO:486, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:500, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:515, SEQ ID NO:534, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:544, SEQ ID NO:552, SEQ ID NO:562, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:573, SEQ ID NO:577, SEQ ID NO:580, SEQ ID NO:592, SEQ ID NO:595, SEQ ID NO:602, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:649, SEQ ID NO:655, SEQ ID NO:658, SEQ ID NO:664, SEQ ID NO:674, SEQ ID NO:681, SEQ ID NO:683, SEQ ID NO:699, SEQ ID NO:704, SEQ ID NO:708, SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:717, SEQ ID NO:719, SEQ ID NO:721, SEQ ID NO:723, SEQ ID NO:746, SEQ ID NO:752, SEQ ID NO:754, SEQ ID NO:764, SEQ ID NO:785, SEQ ID NO:789, SEQ ID NO:795, SEQ ID NO:797, SEQ ID NO:799, SEQ ID NO:801, SEQ ID NO:810, SEQ ID NO:819, SEQ ID NO:821, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:829, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:848, SEQ ID NO:854, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:867, SEQ ID NO:889, SEQ ID NO:891, SEQ ID NO:893, SEQ ID NO:895, SEQ ID NO:903, SEQ ID NO:906, SEQ ID NO:911, SEQ ID NO:916, SEQ ID NO:918, SEQ ID NO:920, SEQ ID NO:926, SEQ ID NO:928, SEQ ID NO:942, SEQ ID NO:944, SEQ ID NO:958, SEQ ID NO:965, SEQ ID NO:967, SEQ ID NO:972, SEQ ID NO:974, SEQ ID NO:981, SEQ ID NO:1006, SEQ ID NO:1010, SEQ ID NO:1015, SEQ ID NO:1027, SEQ ID NO:1030, SEQ ID NO:1034, SEQ ID NO:1054, SEQ ID NO:1067, SEQ ID NO:1070, SEQ ID NO:1077, SEQ ID NO:1084, SEQ ID NO:1086, SEQ ID NO:1090, SEQ ID NO:1093, SEQ ID NO:1097, SEQ ID NO:1108, SEQ ID NO:1116, SEQ ID NO:1121, SEQ ID NO:1124, SEQ ID NO:1138, SEQ ID NO:1142, SEQ ID NO:1148, SEQ ID NO:1155, SEQ ID NO:1158, SEQ ID NO:1160, SEQ ID NO:1170, SEQ ID NO:1172, SEQ ID NO:1175, SEQ ID NO:1208, SEQ ID NO:1212, SEQ ID NO:1214, SEQ ID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1236, SEQ ID NO:1240, SEQ ID NO:1242, SEQ ID NO:1244, SEQ ID NO:1246, SEQ ID NO:1250, SEQ ID NO:1252, SEQ ID NO:1254, SEQ ID NO:1256, SEQ ID NO:1260, SEQ ID NO:1262, SEQ ID NO:1264, SEQ ID NO:1268, SEQ ID NO:1270, SEQ ID NO:1272, SEQ ID NO:1274, SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1282, SEQ ID NO:1291, SEQ ID NO:1295, SEQ ID NO:1297, SEQ ID NO:1299, SEQ ID NO:1310, SEQ ID NO:1312, SEQ ID NO:1316, SEQ ID NO:1318, SEQ ID NO:1320, SEQ ID NO:1324, SEQ ID NO:1326, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1334, SEQ ID NO:1336, SEQ ID NO:1338, SEQ ID NO:1340, SEQ ID NO:1342, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1356, SEQ ID NO:1358, SEQ ID NO:1368, SEQ ID NO:1372, SEQ ID NO:1374, SEQ ID NO:1378, SEQ ID NO:1380, SEQ ID NO:1384, SEQ ID NO:1386, SEQ ID NO:1388, SEQ ID NO:1390, SEQ ID NO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1402, SEQ ID NO:1411, SEQ ID NO:1416, SEQ ID NO:1418, SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1466, SEQ ID NO:1470, SEQ ID NO:1476, SEQ ID NO:1478, SEQ ID NO:1482, SEQ ID NO:1484, SEQ ID NO:1486, SEQ ID NO:1501, SEQ ID NO:1519, SEQ ID NO:1521, SEQ ID NO:1523, SEQ ID NO:1527, SEQ ID NO:1535, SEQ ID NO:1537, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1549, SEQ ID NO:1553, SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID NO:1574, SEQ ID NO:1576, SEQ ID NO:1578, SEQ ID NO:1582, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1623, SEQ ID NO:1625, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1656, SEQ ID NO:1658, SEQ ID NO:1662, SEQ ID NO:1664, SEQ ID NO:1666, SEQ ID NO:1668, SEQ ID NO:1670, SEQ ID NO:1672, SEQ ID NO:1682, SEQ ID NO:1693, SEQ ID NO:1695, SEQ ID NO:1699, SEQ ID NO:1701, SEQ ID NO:1703, SEQ ID NO:1705, SEQ ID NO:1707, SEQ ID NO:1709, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1715, SEQ ID NO:1717, SEQ ID NO:1719, SEQ ID NO:1723, SEQ ID NO:1725, SEQ ID NO:1732, SEQ ID NO:1748, SEQ ID NO:1776, SEQ ID NO:1780, SEQ ID NO:1782, SEQ ID NO:1833, SEQ ID NO:1855, SEQ ID NO:1891, SEQ ID NO:1898, SEQ ID NO:1900, SEQ ID NO:1907, SEQ ID NO:2060, SEQ ID NO:2062, SEQ ID NO:2064, SEQ ID NO:2088, SEQ ID NO:2090, SEQ ID NO:2092, SEQ ID NO:2094, SEQ ID NO:2096, SEQ ID NO:2098, SEQ ID NO:2100, SEQ ID NO:2102, SEQ ID NO:2104, SEQ ID NO:2106, SEQ ID NO:2108, SEQ ID NO:2110, SEQ ID NO:2112, SEQ ID NO:2114, SEQ ID NO:2116, SEQ ID NO:2118, SEQ ID NO:2120, SEQ ID NO:2122, SEQ ID NO:2124, SEQ ID NO:2126, SEQ ID NO:2128, SEQ ID NO:2130, SEQ ID NO:2132, SEQ ID NO:2134, SEQ ID NO:2136, SEQ ID NO:2138, SEQ ID NO:2140, SEQ ID NO:2142, SEQ ID NO:2144, SEQ ID NO:2146, SEQ ID NO:2148, SEQ ID NO:2150, SEQ ID NO:2152, SEQ ID NO:2154, SEQ ID NO:2156, SEQ ID NO:2158, SEQ ID NO:2160, SEQ ID NO:2161, SEQ ID NO:2163, SEQ ID NO:2165, SEQ ID NO:6167, SEQ ID NO:2169, SEQ ID NO:2171, SEQ ID NO:2173, SEQ ID NO:2175, SEQ ID NO:2177, SEQ ID NO:2179, SEQ ID NO:2181, SEQ ID NO:2183, SEQ ID NO:2185, SEQ ID NO:2187, SEQ ID NO:2189, SEQ ID NO:2191, SEQ ID NO:2193, SEQ ID NO:2195, SEQ ID NO:2197, SEQ ID NO:2199, SEQ ID NO:2201, SEQ ID NO:2203, SEQ ID NO:2205, SEQ ID NO:2207, SEQ ID NO:2209, SEQ ID NO:2211, SEQ ID NO:2213, SEQ ID NO:2215, SEQ ID NO:2217, SEQ ID NO:2219, SEQ ID NO:2221, SEQ ID NO:2223, SEQ ID NO:2225, SEQ ID NO:2227, SEQ ID NO:2229, SEQ ID NO:2231, SEQ ID NO:2233, SEQ ID NO:2235, SEQ ID NO:2237, SEQ ID NO:2239, SEQ ID NO:2241, SEQ ID NO:2243, SEQ ID NO:2245, SEQ ID NO:2247, SEQ ID NO:2249, SEQ ID NO:2251, SEQ ID NO:2253, SEQ ID NO:2255, SEQ ID NO:2257, SEQ ID NO:2259, SEQ ID NO:2261, SEQ ID NO:2263, SEQ ID NO:2265, SEQ ID NO:2267, SEQ ID NO:2269, SEQ ID NO:2271, SEQ ID NO:2273, SEQ ID NO:2275, SEQ ID NO:2277, SEQ ID NO:2279, SEQ ID NO:2281, SEQ ID NO:2283, SEQ ID NO:2285, SEQ ID NO:2287, SEQ ID NO:2289, SEQ ID NO:2291, SEQ ID NO:2293, SEQ ID NO:2295, SEQ ID NO:2297, SEQ ID NO:2299, SEQ ID NO:2301, SEQ ID NO:2303, SEQ ID NO:2305, SEQ ID NO:2307, SEQ ID NO:2309, SEQ ID NO:2311, SEQ ID NO:2313, SEQ ID NO:2315, SEQ ID NO:2317, SEQ ID NO:2319, SEQ ID NO:2321, SEQ ID NO:2323, SEQ ID NO:2325, SEQ ID NO:2327, SEQ ID NO:2329, SEQ ID NO:2331, SEQ ID NO:2333, SEQ ID NO:2335, SEQ ID NO:2337, SEQ ID NO:2339, SEQ ID NO:2341, SEQ ID NO:2343, SEQ ID NO:2345, SEQ ID NO:2347, or SEQ ID NO:2690.

In another aspect, a method of modulating the lignin content in a plant is provided. The method comprises introducing into a plant cell an exogenous nucleic acid comprising a regulatory region operably linked to a nucleic acid having 95% or greater sequence identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:118, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:129, SEQ ID NO:133, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:148, SEQ ID NO:150, SEQ ID NO:156, SEQ ID NO:158, SEQ ID NO:160, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:169, SEQ ID NO:171, SEQ ID NO:177, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:271, SEQ ID NO:274, SEQ ID NO:278, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:314, SEQ ID NO:317, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:327, SEQ ID NO:329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:336, SEQ ID NO:338, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:352, SEQ ID NO:354, SEQ ID NO:356, SEQ ID NO:360, SEQ ID NO:369, SEQ ID NO:371, SEQ ID NO:373, SEQ ID NO:376, SEQ ID NO:378, SEQ ID NO:380, SEQ ID NO:386, SEQ ID NO:390, SEQ ID NO:393, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID NO:416, SEQ ID NO:431, SEQ ID NO:435, SEQ ID NO:437, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:444, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:453, SEQ ID NO:458, SEQ ID NO:460, SEQ ID NO:464, SEQ ID NO:469, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:477, SEQ ID NO:482, SEQ ID NO:486, SEQ ID NO:489, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:500, SEQ ID NO:503, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:515, SEQ ID NO:517, SEQ ID NO:519, SEQ ID NO:523, SEQ ID NO:525, SEQ ID NO:528, SEQ ID NO:534, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:544, SEQ ID NO:547, SEQ ID NO:552, SEQ ID NO:554, SEQ ID NO:562, SEQ ID NO:565, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:573, SEQ ID NO:577, SEQ ID NO:580, SEQ ID NO:582, SEQ ID NO:584, SEQ ID NO:589, SEQ ID NO:592, SEQ ID NO:595, SEQ ID NO:598, SEQ ID NO:600, SEQ ID NO:602, SEQ ID NO:605, SEQ ID NO:607, SEQ ID NO:609, SEQ ID NO:611, SEQ ID NO:613, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:637, SEQ ID NO:649, SEQ ID NO:651, SEQ ID NO:655, SEQ ID NO:658, SEQ ID NO:660, SEQ ID NO:664, SEQ ID NO:670, SEQ ID NO:674, SEQ ID NO:677, SEQ ID NO:679, SEQ ID NO:681, SEQ ID NO:683, SEQ ID NO:685, SEQ ID NO:688, SEQ ID NO:694, SEQ ID NO:697, SEQ ID NO:699, SEQ ID NO:702, SEQ ID NO:704, SEQ ID NO:706, SEQ ID NO:708, SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:717, SEQ ID NO:719, SEQ ID NO:721, SEQ ID NO:723, SEQ ID NO:729, SEQ ID NO:736, SEQ ID NO:741, SEQ ID NO:743, SEQ ID NO:746, SEQ ID NO:752, SEQ ID NO:754, SEQ ID NO:759, SEQ ID NO:764, SEQ ID NO:778, SEQ ID NO:780, SEQ ID NO:785, SEQ ID NO:789, SEQ ID NO:792, SEQ ID NO:795, SEQ ID NO:797, SEQ ID NO:799, SEQ ID NO:801, SEQ ID NO:807, SEQ ID NO:810, SEQ ID NO:813, SEQ ID NO:815, SEQ ID NO:819, SEQ ID NO:821, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:829, SEQ ID NO:832, SEQ ID NO:834, SEQ ID NO:837, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:848, SEQ ID NO:851, SEQ ID NO:854, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:864, SEQ ID NO:867, SEQ ID NO:884, SEQ ID NO:889, SEQ ID NO:891, SEQ ID NO:893, SEQ ID NO:895, SEQ ID NO:897, SEQ ID NO:899, SEQ ID NO:903, SEQ ID NO:906, SEQ ID NO:911, SEQ ID NO:913, SEQ ID NO:916, SEQ ID NO:918, SEQ ID NO:920, SEQ ID NO:926, SEQ ID NO:928, SEQ ID NO:933, SEQ ID NO:935, SEQ ID NO:937, SEQ ID NO:942, SEQ ID NO:944, SEQ ID NO:958, SEQ ID NO:963, SEQ ID NO:965, SEQ ID NO:967, SEQ ID NO:972, SEQ ID NO:974, SEQ ID NO:979, SEQ ID NO:981, SEQ ID NO:993, SEQ ID NO:1006, SEQ ID NO:1010, SEQ ID NO:1015, SEQ ID NO:1027, SEQ ID NO:1030, SEQ ID NO:1034, SEQ ID NO:1049, SEQ ID NO:1051, SEQ ID NO:1054, SEQ ID NO:1057, SEQ ID NO:1059, SEQ ID NO:1061, SEQ ID NO:1063, SEQ ID NO:1067, SEQ ID NO:1070, SEQ ID NO:1077, SEQ ID NO:1080, SEQ ID NO:1082, SEQ ID NO:1084, SEQ ID NO:1086, SEQ ID NO:1090, SEQ ID NO:1093, SEQ ID NO:1095, SEQ ID NO:1097, SEQ ID NO:1103, SEQ ID NO:1108, SEQ ID NO:1116, SEQ ID NO:1121, SEQ ID NO:1124, SEQ ID NO:1128, SEQ ID NO:1130, SEQ ID NO:1133, SEQ ID NO:1135, SEQ ID NO:1138, SEQ ID NO:1142, SEQ ID NO:1148, SEQ ID NO:1155, SEQ ID NO:1158, SEQ ID NO:1160, SEQ ID NO:1162, SEQ ID NO:1164, SEQ ID NO:1170, SEQ ID NO:1172, SEQ ID NO:1175, SEQ ID NO:1182, SEQ ID NO:1184, SEQ ID NO:1208, SEQ ID NO:1210, SEQ ID NO:1212, SEQ ID NO:1214, SEQ ID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1236, SEQ ID NO:1238, SEQ ID NO:1240, SEQ ID NO:1242, SEQ ID NO:1244, SEQ ID NO:1246, SEQ ID NO:1248, SEQ ID NO:1250, SEQ ID NO:1252, SEQ ID NO:1254, SEQ ID NO:1256, SEQ ID NO:1258, SEQ ID NO:1260, SEQ ID NO:1262, SEQ ID NO:1264, SEQ ID NO:1266, SEQ ID NO:1268, SEQ ID NO:1270, SEQ ID NO:1272, SEQ ID NO:1274, SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1282, SEQ ID NO:1284, SEQ ID NO:1291, SEQ ID NO:1293, SEQ ID NO:1295, SEQ ID NO:1297, SEQ ID NO:1299, SEQ ID NO:1301, SEQ ID NO:1310, SEQ ID NO:1312, SEQ ID NO:1314, SEQ ID NO:1316, SEQ ID NO:1318, SEQ ID NO:1320, SEQ ID NO:1322, SEQ ID NO:1324, SEQ ID NO:1326, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1332, SEQ ID NO:1334, SEQ ID NO:1336, SEQ ID NO:1338, SEQ ID NO:1340, SEQ ID NO:1342, SEQ ID NO:1344, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1356, SEQ ID NO:1358, SEQ ID NO:1360, SEQ ID NO:1368, SEQ ID NO:1370, SEQ ID NO:1372, SEQ ID NO:1374, SEQ ID NO:1376, SEQ ID NO:1378, SEQ ID NO:1380, SEQ ID NO:1382, SEQ ID NO:1384, SEQ ID NO:1386, SEQ ID NO:1388, SEQ ID NO:1390, SEQ ID NO:1392, SEQ ID NO:1394, SEQ ID NO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1402, SEQ ID NO:1404, SEQ ID NO:1411, SEQ ID NO:1413, SEQ ID NO:1416, SEQ ID NO:1418, SEQ ID NO:1420, SEQ ID NO:1422, SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1434, SEQ ID NO:1435, SEQ ID NO:1443, SEQ ID NO:1464, SEQ ID NO:1466, SEQ ID NO:1468, SEQ ID NO:1470, SEQ ID NO:1472, SEQ ID NO:1474, SEQ ID NO:1476, SEQ ID NO:1478, SEQ ID NO:1480, SEQ ID NO:1482, SEQ ID NO:1484, SEQ ID NO:1486, SEQ ID NO:1492, SEQ ID NO:1501, SEQ ID NO:1503, SEQ ID NO:1517, SEQ ID NO:1519, SEQ ID NO:1521, SEQ ID NO:1523, SEQ ID NO:1525, SEQ ID NO:1527, SEQ ID NO:1535, SEQ ID NO:1537, SEQ ID NO:1539, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1549, SEQ ID NO:1551, SEQ ID NO:1553, SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1563, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID NO:1569, SEQ ID NO:1572, SEQ ID NO:1574, SEQ ID NO:1576, SEQ ID NO:1578, SEQ ID NO:1580, SEQ ID NO:1582, SEQ ID NO:1584, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1594, SEQ ID NO:1609, SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1619, SEQ ID NO:1623, SEQ ID NO:1625, SEQ ID NO:1627, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1636, SEQ ID NO:1652, SEQ ID NO:1656, SEQ ID NO:1658, SEQ ID NO:1660, SEQ ID NO:1662, SEQ ID NO:1664, SEQ ID NO:1666, SEQ ID NO:1668, SEQ ID NO:1670, SEQ ID NO:1672, SEQ ID NO:1674, SEQ ID NO:1680, SEQ ID NO:1682, SEQ ID NO:1691, SEQ ID NO:1693, SEQ ID NO:1695, SEQ ID NO:1697, SEQ ID NO:1699, SEQ ID NO:1701, SEQ ID NO:1703, SEQ ID NO:1705, SEQ ID NO:1707, SEQ ID NO:1709, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1715, SEQ ID NO:1717, SEQ ID NO:1719, SEQ ID NO:1721, SEQ ID NO:1723, SEQ ID NO:1725, SEQ ID NO:1727, SEQ ID NO:1732, SEQ ID NO:1734, SEQ ID NO:1748, SEQ ID NO:1751, SEQ ID NO:1766, SEQ ID NO:1776, SEQ ID NO:1778, SEQ ID NO:1780, SEQ ID NO:1782, SEQ ID NO:1784, SEQ ID NO:1805, SEQ ID NO:1821, SEQ ID NO:1823, SEQ ID NO:1825, SEQ ID NO:1827, SEQ ID NO:1829, SEQ ID NO:1831, SEQ ID NO:1833, SEQ ID NO:1835, SEQ ID NO:1837, SEQ ID NO:1839, SEQ ID NO:1841, SEQ ID NO:1843, SEQ ID NO:1845, SEQ ID NO:1847, SEQ ID NO:1849, SEQ ID NO:1851, SEQ ID NO:1853, SEQ ID NO:1855, SEQ ID NO:1857, SEQ ID NO:1859, SEQ ID NO:1861, SEQ ID NO:1863, SEQ ID NO:1865, SEQ ID NO:1867, SEQ ID NO:1869, SEQ ID NO:1871, SEQ ID NO:1873, SEQ ID NO:1875, SEQ ID NO:1877, SEQ ID NO:1879, SEQ ID NO:1881, SEQ ID NO:1883, SEQ ID NO:1885, SEQ ID NO:1887, SEQ ID NO:1889, SEQ ID NO:1891, SEQ ID NO:1896, SEQ ID NO:1898, SEQ ID NO:1900, SEQ ID NO:1903, SEQ ID NO:1905, SEQ ID NO:1907, SEQ ID NO:1919, SEQ ID NO:1920, SEQ ID NO:2060, SEQ ID NO:2062, SEQ ID NO:2064, SEQ ID NO:2084, SEQ ID NO:2088, SEQ ID NO:2090, SEQ ID NO:2092, SEQ ID NO:2094, SEQ ID NO:2096, SEQ ID NO:2098, SEQ ID NO:2100, SEQ ID NO:2102, SEQ ID NO:2104, SEQ ID NO:2106, SEQ ID NO:2108, SEQ ID NO:2110, SEQ ID NO:2112, SEQ ID NO:2114, SEQ ID NO:2116, SEQ ID NO:2118, SEQ ID NO:2120, SEQ ID NO:2122, SEQ ID NO:2124, SEQ ID NO:2126, SEQ ID NO:2128, SEQ ID NO:2130, SEQ ID NO:2132, SEQ ID NO:2134, SEQ ID NO:2136, SEQ ID NO:2138, SEQ ID NO:2140, SEQ ID NO:2142, SEQ ID NO:2144, SEQ ID NO:2146, SEQ ID NO:2148, SEQ ID NO:2150, SEQ ID NO:2152, SEQ ID NO:2154, SEQ ID NO:2156, SEQ ID NO:2158, SEQ ID NO:2160, SEQ ID NO:2161, SEQ ID NO:2163, SEQ ID NO:2165, SEQ ID NO:6167, SEQ ID NO:2169, SEQ ID NO:2171, SEQ ID NO:2173, SEQ ID NO:2175, SEQ ID NO:2177, SEQ ID NO:2179, SEQ ID NO:2181, SEQ ID NO:2183, SEQ ID NO:2185, SEQ ID NO:2187, SEQ ID NO:2189, SEQ ID NO:2191, SEQ ID NO:2193, SEQ ID NO:2195, SEQ ID NO:2197, SEQ ID NO:2199, SEQ ID NO:2201, SEQ ID NO:2203, SEQ ID NO:2205, SEQ ID NO:2207, SEQ ID NO:2209, SEQ ID NO:2211, SEQ ID NO:2213, SEQ ID NO:2215, SEQ ID NO:2217, SEQ ID NO:2219, SEQ ID NO:2221, SEQ ID NO:2223, SEQ ID NO:2225, SEQ ID NO:2227, SEQ ID NO:2229, SEQ ID NO:2231, SEQ ID NO:2233, SEQ ID NO:2235, SEQ ID NO:2237, SEQ ID NO:2239, SEQ ID NO:2241, SEQ ID NO:2243, SEQ ID NO:2245, SEQ ID NO:2247, SEQ ID NO:2249, SEQ ID NO:2251, SEQ ID NO:2253, SEQ ID NO:2255, SEQ ID NO:2257, SEQ ID NO:2259, SEQ ID NO:2261, SEQ ID NO:2263, SEQ ID NO:2265, SEQ ID NO:2267, SEQ ID NO:2269, SEQ ID NO:2271, SEQ ID NO:2273, SEQ ID NO:2275, SEQ ID NO:2277, SEQ ID NO:2279, SEQ ID NO:2281, SEQ ID NO:2283, SEQ ID NO:2285, SEQ ID NO:2287, SEQ ID NO:2289, SEQ ID NO:2291, SEQ ID NO:2293, SEQ ID NO:2295, SEQ ID NO:2297, SEQ ID NO:2299, SEQ ID NO:2301, SEQ ID NO:2303, SEQ ID NO:2305, SEQ ID NO:2307, SEQ ID NO:2309, SEQ ID NO:2311, SEQ ID NO:2313, SEQ ID NO:2315, SEQ ID NO:2317, SEQ ID NO:2319, SEQ ID NO:2321, SEQ ID NO:2323, SEQ ID NO:2325, SEQ ID NO:2327, SEQ ID NO:2329, SEQ ID NO:2331, SEQ ID NO:2333, SEQ ID NO:2335, SEQ ID NO:2337, SEQ ID NO:2339, SEQ ID NO:2341, SEQ ID NO:2343, SEQ ID NO:2345, SEQ ID NO:2347, and SEQ ID NO:2349-2690; where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

FIG. 1 is an alignment of the amino acid sequence of Annot ID 541887 (SEQ ID NO:96) with homologous and/or orthologous amino acid sequences CeresAnnot:1448288 (SEQ ID NO:98), CeresClone:644583 (SEQ ID NO:99), gi|50926522 (SEQ ID NO:100), and CeresClone:1791381 (SEQ ID NO:102). In all the alignment figures shown herein, a dash in an aligned sequence represents a gap, i.e., a lack of an amino acid at that position. Identical amino acids or conserved amino acid substitutions among aligned sequences are identified by boxes. FIG. 1 and the other alignment figures provided herein were generated using the program MUSCLE version 3.52.

FIG. 2 is an alignment of the amino acid sequence of Annot ID 548715 (SEQ ID NO:106) with homologous and/or orthologous amino acid sequences CeresAnnot:1447956 (SEQ ID NO:108), CeresClone:1923054 (SEQ ID NO:110), CeresClone:1051305 (SEQ ID NO:111), gi|50923813 (SEQ ID NO:112), CeresClone:1746793 (SEQ ID NO:114), CeresClone:843382 (SEQ ID NO:115), and CeresClone:1540519 (SEQ ID NO:116).

FIG. 3 is an alignment of the amino acid sequence of Annot ID 549656 (SEQ ID NO:119) with homologous and/or orthologous amino acid sequences CeresClone:463643 (SEQ ID NO:122), CeresAnnot:1442640 (SEQ ID NO:124), CeresClone:704938 (SEQ ID NO:127), CeresClone:281395 (SEQ ID NO:128), CeresClone:1784166 (SEQ ID NO:130), and gi|56785216 (SEQ ID NO:131).

FIG. 4 is an alignment of the amino acid sequence of Annot ID 550729 (SEQ ID NO:134) with homologous and/or orthologous amino acid sequences gi|20340241 (SEQ ID NO:136), CeresClone:473509 (SEQ ID NO:137), CeresAnnot:1525600 (SEQ ID NO:139), CeresClone:1922929 (SEQ ID NO:141), gi|76446335 (SEQ ID NO:146), and gi|37901055 (SEQ ID NO:147).

FIG. 5 is an alignment of the amino acid sequence of Annot ID 554970 (SEQ ID NO:149) with homologous and/or orthologous amino acid sequences CeresAnnot:1528227 (SEQ ID NO:151), gi|34908948 (SEQ ID NO:152), and CeresClone:1158508 (SEQ ID NO:154).

FIG. 6 is an alignment of the amino acid sequence of Annot ID 840236 (SEQ ID NO:165) with homologous and/or orthologous amino acid sequence gi|21105736 (SEQ ID NO:168).

FIG. 7 is an alignment of the amino acid sequence of CeresClone:1001761 (SEQ ID NO:172) with homologous and/or orthologous amino acid sequences CeresClone:955105 (SEQ ID NO:174) and CeresClone:1620054 (SEQ ID NO:175).

FIG. 8 is an alignment of the amino acid sequence of CeresClone:1003205 (SEQ ID NO:178) with homologous and/or orthologous amino acid sequences CeresClone:1120014 (SEQ ID NO:179), CeresClone:1066826 (SEQ ID NO:180), CeresClone:1465358 (SEQ ID NO:185), gi|18347 (SEQ ID NO:186), CeresClone:1012773 (SEQ ID NO:190), gi|1346180 (SEQ ID NO:192), gi|469070 (SEQ ID NO:194), CeresAnnot:1450324 (SEQ ID NO:196), gi|2624326 (SEQ ID NO:199), CeresClone:815584 (SEQ ID NO:201), and CeresClone:1898837 (SEQ ID NO:217).

FIG. 9 is an alignment of the amino acid sequence of CeresClone:1011900 (SEQ ID NO:221) with homologous and/or orthologous amino acid sequences CeresClone:1083222 (SEQ ID NO:222), CeresClone:1075035 (SEQ ID NO:223), CeresClone:1444599 (SEQ ID NO:225), gi|1346181 (SEQ ID NO:227), CeresClone:1053672 (SEQ ID NO:231), gi|469070 (SEQ ID NO:232), gi|2226370 (SEQ ID NO:234), gi|2267569 (SEQ ID NO:235), gi|18347 (SEQ ID NO:244), gi|34851124 (SEQ ID NO:246), gi|7024451 (SEQ ID NO:247), gi|6273331 (SEQ ID NO:248), gi|20152613 (SEQ ID NO:249), gi|92874469 (SEQ ID NO:250), CeresAnnot:1450324 (SEQ ID NO:253), gi|1229138 (SEQ ID NO:256), CeresClone:1834392 (SEQ ID NO:258), gi|108863012 (SEQ ID NO:263), gi|6911144 (SEQ ID NO:270), CeresClone:1773631 (SEQ ID NO:275), gi|1934994 (SEQ ID NO:290), gi|2674201 (SEQ ID NO:296), gi|799015 (SEQ ID NO:297), gi|4704605 (SEQ ID NO:311), gi|10799202 (SEQ ID NO:313), gi|90265701 (SEQ ID NO:316), gi|90704785 (SEQ ID NO:319), gi|21625 (SEQ ID NO:326), and gi|21388658 (SEQ ID NO:335).

FIG. 10 is an alignment of the amino acid sequence of CeresClone:105162 (SEQ ID NO:339) with homologous and/or orthologous amino acid sequences CeresClone:1853694 (SEQ ID NO:343), CeresAnnot:1494468 (SEQ ID NO:345), gi|38036140 (SEQ ID NO:348), CeresClone:1649800 (SEQ ID NO:349), CeresClone:984060 (SEQ ID NO:350), gi|31872116 (SEQ ID NO:351), and CeresClone:1816624 (SEQ ID NO:353).

FIG. 11 is an alignment of the amino acid sequence of CeresClone:110428 (SEQ ID NO:357) with homologous and/or orthologous amino acid sequence CeresClone:1444428 (SEQ ID NO:359).

FIG. 12 is an alignment of the amino acid sequence of CeresClone:112098 (SEQ ID NO:361) with homologous and/or orthologous amino acid sequences CeresClone:1376604 (SEQ ID NO:367) and CeresClone:463184 (SEQ ID NO:368).

FIG. 13 is an alignment of the amino acid sequence of CeresClone:113639 (SEQ ID NO:374) with homologous and/or orthologous amino acid sequences CeresClone:562894 (SEQ ID NO:375) and CeresAnnot:1503065 (SEQ ID NO:377).

FIG. 14 is an alignment of the amino acid sequence of CeresClone:115366 (SEQ ID NO:381) with homologous and/or orthologous amino acid sequences CeresClone:1376400 (SEQ ID NO:382), CeresClone:1834350 (SEQ ID NO:387), CeresClone:518274 (SEQ ID NO:389), gi|82400162 (SEQ ID NO:392), CeresAnnot:1446310 (SEQ ID NO:394), gi|6996560 (SEQ ID NO:395), gi|77551976 (SEQ ID NO:396), gi|92891800 (SEQ ID NO:398), CeresClone:1790416 (SEQ ID NO:400), and CeresClone:703017 (SEQ ID NO:403).

FIG. 15 is an alignment of the amino acid sequence of CeresClone:12256 (SEQ ID NO:417) with homologous and/or orthologous amino acid sequences CeresClone:976830 (SEQ ID NO:418), gi|87240462 (SEQ ID NO:421), gi|77556133 (SEQ ID NO:422), CeresClone:305612 (SEQ ID NO:423), CeresClone:686862 (SEQ ID NO:424), and CeresClone:1113246 (SEQ ID NO:425).

FIG. 16 is an alignment of the amino acid sequence of CeresClone:123804 (SEQ ID NO:432) with homologous and/or orthologous amino acid sequence CeresClone:670908 (SEQ ID NO:433).

FIG. 17 is an alignment of the amino acid sequence of CeresClone:125917 (SEQ ID NO:438) with homologous and/or orthologous amino acid sequences CeresAnnot:1456569 (SEQ ID NO:440), CeresAnnot:1450998 (SEQ ID NO:442), and gi|92873189 (SEQ ID NO:443).

FIG. 18 is an alignment of the amino acid sequence of Ceres Clone 14203 (SEQ ID NO:445) with homologous and/or orthologous amino acid sequences CeresClone:1021029 (SEQ ID NO:446), CeresClone:974951 (SEQ ID NO:447), 1460527 (SEQ ID NO:449), CeresClone:1853189 (SEQ ID NO:451), gi|92896423 (SEQ ID NO:452), CeresClone:1853430 (SEQ ID NO:454), CeresClone:1734621 (SEQ ID NO:455), gi|50909195 (SEQ ID NO:456), gi|66271037 (SEQ ID NO:457), and 1450673 (SEQ ID NO:459).

FIG. 19 is an alignment of the amino acid sequence of CeresClone:1480 (SEQ ID NO:461) with homologous and/or orthologous amino acid sequences CeresClone:1067639 (SEQ ID NO:462) and CeresClone:1068473 (SEQ ID NO:463).

FIG. 20 is an alignment of the amino acid sequence of CeresClone:1492 (SEQ ID NO:465) with homologous and/or orthologous amino acid sequences gi|89257443 (SEQ ID NO:466), CeresClone:1128644 (SEQ ID NO:467), gi|4586580 (SEQ ID NO:468), CeresClone:1835140 (SEQ ID NO:470), gi|50911379 (SEQ ID NO:471), 1538756 (SEQ ID NO:473), CeresClone:1840642 (SEQ ID NO:475), gi|311907 (SEQ ID NO:476), CeresClone:1932400 (SEQ ID NO:478), gi|1053067 (SEQ ID NO:479), CeresClone:727613 (SEQ ID NO:480), gi|34914060 (SEQ ID NO:481), CeresClone:1834939 (SEQ ID NO:483), gi|2500073 (SEQ ID NO:484), gi|5902803 (SEQ ID NO:485), CeresClone:1785552 (SEQ ID NO:487), and gi|401686 (SEQ ID NO:488).

FIG. 21 is an alignment of the amino acid sequence of Ceres Clone 156298 (SEQ ID NO:490) with homologous and/or orthologous amino acid sequences CeresAnnot:1512948 (SEQ ID NO:492), CeresClone:659211 (SEQ ID NO:497), gi|92877546 (SEQ ID NO:498), CeresClone:1831324 (SEQ ID NO:501), and CeresClone:398632 (SEQ ID NO:502). The consensus sequence determined by the alignment is set forth

FIG. 22 is an alignment of the amino acid sequence of Ceres Clone 156373 (SEQ ID NO:504) with homologous and/or orthologous amino acid sequences CeresClone:1393778 (SEQ ID NO:505), CeresAnnot:1518013 (SEQ ID NO:508), CeresClone:477995 (SEQ ID NO:511), gi|45387429 (SEQ ID NO:513), gi|34900462 (SEQ ID NO:514), and CeresClone:1826835 (SEQ ID NO:516).

FIG. 23 is an alignment of the amino acid sequence of Ceres Clone 158240 (SEQ ID NO:520) with homologous and/or orthologous amino acid sequences gi|37538128 (SEQ ID NO:521) and gi|84453218 (SEQ ID NO:522).

FIG. 24 is an alignment of the amino acid sequence of Ceres Clone 16284 (SEQ ID NO:526) with homologous and/or orthologous amino acid sequence CeresClone:976709 (SEQ ID NO:527).

FIG. 25 is an alignment of the amino acid sequence of Ceres Clone 17402 (SEQ ID NO:529) with homologous and/or orthologous amino acid sequences CeresClone:1432566 (SEQ ID NO:530), CeresClone:1500962 (SEQ ID NO:531), CeresClone:1387733 (SEQ ID NO:532), CeresClone:1408748 (SEQ ID NO:533), CeresClone:1834915 (SEQ ID NO:535), CeresClone:1841007 (SEQ ID NO:537), CeresClone:1836048 (SEQ ID NO:539), CeresAnnot:1541305 (SEQ ID NO:541), CeresAnnot:1487895 (SEQ ID NO:543), CeresAnnot:1510353 (SEQ ID NO:545), and gi|68299223 (SEQ ID NO:546).

FIG. 26 is an alignment of the amino acid sequence of Ceres Clone 1845 (SEQ ID NO:548) with homologous and/or orthologous amino acid sequences CeresClone:890211 (SEQ ID NO:549), CeresClone:556120 (SEQ ID NO:550), and CeresAnnot:1483577 (SEQ ID NO:553).

FIG. 27 is an alignment of the amino acid sequence of Ceres Clone 205648 (SEQ ID NO:555) with homologous and/or orthologous amino acid sequences gi|102139801 (SEQ ID NO:556), gi|15148912 (SEQ ID NO:557), CeresClone:577178 (SEQ ID NO:558), CeresClone:644344 (SEQ ID NO:559), gi|52076897 (SEQ ID NO:560), CeresClone:1674566 (SEQ ID NO:561), CeresAnnot:1456842 (SEQ ID NO:563), and gi|34558777 (SEQ ID NO:564).

FIG. 28 is an alignment of the amino acid sequence of Ceres Clone 21406 (SEQ ID NO:566) with homologous and/or orthologous amino acid sequences gi|24030386 (SEQ ID NO:567), gi|6850309 (SEQ ID NO:568), CeresAnnot:1498288 (SEQ ID NO:572), and CeresAnnot:1471938 (SEQ ID NO:574).

FIG. 29 is an alignment of the amino acid sequence of Ceres Clone 224919 (SEQ ID NO:585) with homologous and/or orthologous amino acid sequences gi|50933495 (SEQ ID NO:586) and CeresClone:1556085 (SEQ ID NO:587).

FIG. 30 is an alignment of the amino acid sequence of Ceres Clone 22671 (SEQ ID NO:590) with homologous and/or orthologous amino acid sequences CeresClone:1079601 (SEQ ID NO:591), 1483277 (SEQ ID NO:593), CeresClone:690625 (SEQ ID NO:594), 1467420 (SEQ ID NO:596), and gi|15042132 (SEQ ID NO:597).

FIG. 31 is an alignment of the amino acid sequence of Ceres Clone 240112 (SEQ ID NO:601) with homologous and/or orthologous amino acid sequences CeresClone:1791988 (SEQ ID NO:603) and gi|50918981 (SEQ ID NO:604).

FIG. 32 is an alignment of the amino acid sequence of Ceres Clone 2831 (SEQ ID NO:614) with homologous and/or orthologous amino acid sequences CeresClone:1385680 (SEQ ID NO:617), CeresAnnot:1497776 (SEQ ID NO:619), gi|9650826 (SEQ ID NO:622), CeresClone:1728175 (SEQ ID NO:623), gi|2244744 (SEQ ID NO:624), CeresClone:676378 (SEQ ID NO:625), gi|77999786 (SEQ ID NO:626), gi|16580132 (SEQ ID NO:627), gi|3986151 (SEQ ID NO:629), gi|77556137 (SEQ ID NO:630), gi|72398495 (SEQ ID NO:631), gi|5901747 (SEQ ID NO:633), gi|40019253 (SEQ ID NO:634), and gi|62898531 (SEQ ID NO:635).

FIG. 33 is an alignment of the amino acid sequence of Ceres Clone 285598 (SEQ ID NO:638) with homologous and/or orthologous amino acid sequences CeresClone:236111 (SEQ ID NO:639), gi|34902144 (SEQ ID NO:640), CeresClone:1315656 (SEQ ID NO:641), gi|45602841 (SEQ ID NO:642), gi|45544873 (SEQ ID NO:643), gi|45758663 (SEQ ID NO:644), gi|62320820 (SEQ ID NO:645), gi|92888885 (SEQ ID NO:647), gi|40807658 (SEQ ID NO:648), and CeresAnnot:1486505 (SEQ ID NO:650).

FIG. 34 is an alignment of the amino acid sequence of Ceres Clone 2898 (SEQ ID NO:652) with homologous and/or orthologous amino acid sequences CeresClone:1716210 (SEQ ID NO:653), CeresClone:1421639 (SEQ ID NO:654), 1443201 (SEQ ID NO:656), CeresClone:749118 (SEQ ID NO:657), and 1450718 (SEQ ID NO:659).

FIG. 35 is an alignment of the amino acid sequence of Ceres Clone 2913 (SEQ ID NO:661) with homologous and/or orthologous amino acid sequences CeresClone:1384592 (SEQ ID NO:662), CeresClone:1121989 (SEQ ID NO:663), 1463575 (SEQ ID NO:665), gi|48209882 (SEQ ID NO:666), gi|48209945 (SEQ ID NO:667), gi|349379 (SEQ ID NO:668), and CeresClone:677386 (SEQ ID NO:669).

FIG. 36 is an alignment of the amino acid sequence of Ceres Clone 2942 (SEQ ID NO:671) with homologous and/or orthologous amino acid sequences CeresClone:1619846 (SEQ ID NO:672), gi|50925955 (SEQ ID NO:673), 1455934 (SEQ ID NO:675), and CeresClone:337432 (SEQ ID NO:676).

FIG. 37 is an alignment of the amino acid sequence of Ceres Clone 31044 (SEQ ID NO:680) with homologous and/or orthologous amino acid sequences 1496976 (SEQ ID NO:682) and 1444027 (SEQ ID NO:684).

FIG. 38 is an alignment of the amino acid sequence of Ceres Clone 312833 (SEQ ID NO:686) with homologous and/or orthologous amino acid sequence gi|50920025 (SEQ ID NO:687).

FIG. 39 is an alignment of the amino acid sequence of Ceres Clone 31322 (SEQ ID NO:689) with homologous and/or orthologous amino acid sequences CeresClone:980901 (SEQ ID NO:690), CeresClone:1030653 (SEQ ID NO:691), CeresClone:956177 (SEQ ID NO:692), and CeresClone:1620744 (SEQ ID NO:693).

FIG. 40 is an alignment of the amino acid sequence of Ceres Clone 325679 (SEQ ID NO:695) with homologous and/or orthologous amino acid sequence gi|50910213 (SEQ ID NO:696).

FIG. 41 is an alignment of the amino acid sequence of Ceres Clone 32754 (SEQ ID NO:698) with homologous and/or orthologous amino acid sequences CeresClone:1855403 (SEQ ID NO:700) and CeresClone:572426 (SEQ ID NO:701).

FIG. 42 is an alignment of the amino acid sequence of Ceres Clone 33139 (SEQ ID NO:703) with homologous and/or orthologous amino acid sequences 1503188 (SEQ ID NO:705) and gi|21386951 (SEQ ID NO:2067).

FIG. 43 is an alignment of the amino acid sequence of Ceres Clone 331755 (SEQ ID NO:707) with homologous and/or orthologous amino acid sequences CeresClone:1775942 (SEQ ID NO:709), gi|34913016 (SEQ ID NO:710), CeresClone:1723374 (SEQ ID NO:711), CeresClone:1847251 (SEQ ID NO:713), gi|38566494 (SEQ ID NO:716), CeresAnnot:1514100 (SEQ ID NO:718), CeresClone:638126 (SEQ ID NO:725), gi|7981380 (SEQ ID NO:726), gi|92894385 (SEQ ID NO:727), and gi|61652985 (SEQ ID NO:728).

FIG. 44 is an alignment of the amino acid sequence of Ceres Clone 33435 (SEQ ID NO:730) with homologous and/or orthologous amino acid sequences CeresClone:116606 (SEQ ID NO:731), CeresClone:1079147 (SEQ ID NO:732), CeresClone:957098 (SEQ ID NO:733), CeresClone:1435704 (SEQ ID NO:734), and CeresClone:1496331 (SEQ ID NO:735).

FIG. 45 is an alignment of the amino acid sequence of Ceres Clone 337432 (SEQ ID NO:737) with homologous and/or orthologous amino acid sequences gi|50925955 (SEQ ID NO:738), CeresClone:1619846 (SEQ ID NO:739), gi|27754217 (SEQ ID NO:740), and CeresAnnot:1509127 (SEQ ID NO:742).

FIG. 46 is an alignment of the amino acid sequence of Ceres Clone 339518 (SEQ ID NO:744) with homologous and/or orthologous amino acid sequences CeresClone:243130 (SEQ ID NO:745), CeresClone:1776411 (SEQ ID NO:747), gi|50911777 (SEQ ID NO:748), gi|100796 (SEQ ID NO:750), CeresAnnot:1500106 (SEQ ID NO:753), gi|23197622 (SEQ ID NO:756), and gi|21279 (SEQ ID NO:758).

FIG. 47 is an alignment of the amino acid sequence of Ceres Clone 34635 (SEQ ID NO:760) with homologous and/or orthologous amino acid sequences gi|6707088 (SEQ ID NO:761), gi|48375197 (SEQ ID NO:762), gi|1561782 (SEQ ID NO:763), CeresClone:1921942 (SEQ ID NO:765), gi|1370276 (SEQ ID NO:766), gi|22665 (SEQ ID NO:767), gi|60858812 (SEQ ID NO:768), gi|82734191 (SEQ ID NO:769), gi|99109361 (SEQ ID NO:770), gi|42795301 (SEQ ID NO:771), gi|83999564 (SEQ ID NO:772), gi|42795285 (SEQ ID NO:773), gi|42795257 (SEQ ID NO:774), gi|16549070 (SEQ ID NO:775), gi|60100348 (SEQ ID NO:776), and gi|5825623 (SEQ ID NO:777).

FIG. 48 is an alignment of the amino acid sequence of Ceres Clone 36370 (SEQ ID NO:781) with homologous and/or orthologous amino acid sequences CeresClone:627169 (SEQ ID NO:784), CeresClone:1724787 (SEQ ID NO:786), gi|34914598 (SEQ ID NO:787), CeresClone:1397168 (SEQ ID NO:788), CeresAnnot:1481678 (SEQ ID NO:790), and CeresClone:704527 (SEQ ID NO:791).

FIG. 49 is an alignment of the amino acid sequence of Ceres Clone 37739 (SEQ ID NO:793) with homologous and/or orthologous amino acid sequences gi|20259555 (SEQ ID NO:794), CeresClone:1754197 (SEQ ID NO:796), CeresClone:1856164 (SEQ ID NO:798), 1488340 (SEQ ID NO:800), CeresClone:1807870 (SEQ ID NO:802), gi|45935145 (SEQ ID NO:803), CeresClone:383227 (SEQ ID NO:804), gi|70664005 (SEQ ID NO:805), and CeresClone:909699 (SEQ ID NO:806).

FIG. 50 is an alignment of the amino acid sequence of Ceres Clone 37980 (SEQ ID NO:808) with homologous and/or orthologous amino acid sequences CeresClone:630887 (SEQ ID NO:809), 1460561 (SEQ ID NO:811), and gi|50919643 (SEQ ID NO:812).

FIG. 51 is an alignment of the amino acid sequence of Ceres Clone 38360 (SEQ ID NO:816) with homologous and/or orthologous amino acid sequences gi|108711626 (SEQ ID NO:817), CeresClone:573293 (SEQ ID NO:818), CeresClone:1825572 (SEQ ID NO:820), 1524357 (SEQ ID NO:822), CeresClone:1819666 (SEQ ID NO:824), gi|50919203 (SEQ ID NO:825), CeresClone:230342 (SEQ ID NO:826), CeresClone:1850953 (SEQ ID NO:828), 1470949 (SEQ ID NO:830), and gi|92897066 (SEQ ID NO:831).

FIG. 52 contains photomicrographs of sections from the basal region of the main stems of wild-type or transgenic Arabidopsis plants 22 to 24 days after germination. The sections were stained using phloroglucinol and Mäule reagents as indicated.

FIG. 53 is an alignment of the amino acid sequence of Ceres Clone 3900 (SEQ ID NO:838) with homologous and/or orthologous amino acid sequences CeresClone:158765 (SEQ ID NO:839), CeresClone:1839717 (SEQ ID NO:841), 1480628 (SEQ ID NO:843), gi|5669656 (SEQ ID NO:844), CeresClone:1329861 (SEQ ID NO:845), CeresClone:537752 (SEQ ID NO:846), CeresClone:1322549 (SEQ ID NO:847), 1533351 (SEQ ID NO:849), and CeresClone:282892 (SEQ ID NO:850).

FIG. 54 is an alignment of the amino acid sequence of Ceres Clone 39855 (SEQ ID NO:852) with homologous and/or orthologous amino acid sequences CeresClone:1065335 (SEQ ID NO:853), CeresClone:1793747 (SEQ ID NO:855), CeresClone:788576 (SEQ ID NO:856), CeresClone:465010 (SEQ ID NO:857), CeresClone:1832492 (SEQ ID NO:859), CeresClone:1801885 (SEQ ID NO:861), CeresClone:1060804 (SEQ ID NO:862), gi|50948587 (SEQ ID NO:863), and gi|20259185 (SEQ ID NO:2066).

FIG. 55 is an alignment of the amino acid sequence of Ceres Clone 40334 (SEQ ID NO:865) with homologous and/or orthologous amino acid sequences gi|67043456 (SEQ ID NO:866), 1452158 (SEQ ID NO:868), gi|4105097 (SEQ ID NO:869), gi|56785938 (SEQ ID NO:870), CeresClone:1625939 (SEQ ID NO:871), gi|12666533 (SEQ ID NO:872), gi|60100344 (SEQ ID NO:873), gi|51832629 (SEQ ID NO:874), CeresClone:474230 (SEQ ID NO:875), gi|454265 (SEQ ID NO:876), gi|53988171 (SEQ ID NO:877), gi|48727608 (SEQ ID NO:878), gi|602902 (SEQ ID NO:879), gi|33338587 (SEQ ID NO:880), gi|4218173 (SEQ ID NO:881), gi|33309888 (SEQ ID NO:882), and gi|84578879 (SEQ ID NO:883).

FIG. 56 is an alignment of the amino acid sequence of Ceres Clone 41634 (SEQ ID NO:885) with homologous and/or orthologous amino acid sequences CeresClone:1360604 (SEQ ID NO:887), CeresClone:1844070 (SEQ ID NO:890), and CeresAnnot:1457905 (SEQ ID NO:892).

FIG. 57 is an alignment of the amino acid sequence of Ceres Clone 478453 (SEQ ID NO:900) with homologous and/or orthologous amino acid sequences CeresClone:1923578 (SEQ ID NO:904), gi|51535194 (SEQ ID NO:905), CeresClone:1956222 (SEQ ID NO:907), CeresClone:291139 (SEQ ID NO:908), and CeresClone:569584 (SEQ ID NO:910).

FIG. 58 is an alignment of the amino acid sequence of Ceres Clone 479006 (SEQ ID NO:914) with homologous and/or orthologous amino acid sequences CeresAnnot:1444387 (SEQ ID NO:917), CeresClone:1886347 (SEQ ID NO:919), gi|13508844 (SEQ ID NO:922), gi|14532902 (SEQ ID NO:923), CeresClone:1858581 (SEQ ID NO:927), CeresClone:630211 (SEQ ID NO:930), CeresClone:1534695 (SEQ ID NO:931), and gi|77551916 (SEQ ID NO:932).

FIG. 59 is an alignment of the amino acid sequence of Ceres Clone 534281 (SEQ ID NO:938) with homologous and/or orthologous amino acid sequences gi|92877732 (SEQ ID NO:939), CeresAnnot:1471100 (SEQ ID NO:943), gi|21280839 (SEQ ID NO:946), gi|50911116 (SEQ ID NO:947), CeresClone:1580901 (SEQ ID NO:950), CeresClone:703763 (SEQ ID NO:954), and CeresClone:1795581 (SEQ ID NO:959).

FIG. 60 is an alignment of the amino acid sequence of Ceres Clone 539801 (SEQ ID NO:964) with homologous and/or orthologous amino acid sequences CeresAnnot:1531585 (SEQ ID NO:966), CeresClone:1209672 (SEQ ID NO:969), and gi|51090847 (SEQ ID NO:971).

FIG. 61 is an alignment of the amino acid sequence of Ceres Clone 542773 (SEQ ID NO:980) with homologous and/or orthologous amino acid sequences CeresClone:1845589 (SEQ ID NO:982), gi|50924820 (SEQ ID NO:983), gi|34452085 (SEQ ID NO:984), gi|1816459 (SEQ ID NO:985), gi|15081463 (SEQ ID NO:986), gi|2959320 (SEQ ID NO:987), and gi|29611976 (SEQ ID NO:988).

FIG. 62 is an alignment of the amino acid sequence of Ceres Clone 543118 (SEQ ID NO:994) with homologous and/or orthologous amino acid sequences gi|871508 (SEQ ID NO:995), gi|1370190 (SEQ ID NO:996), gi|1654144 (SEQ ID NO:998), gi|18447913 (SEQ ID NO:999), gi|92897911 (SEQ ID NO:1000), gi|28973447 (SEQ ID NO:1005), CeresAnnot:1458068 (SEQ ID NO:1007), CeresClone:636809 (SEQ ID NO:1008), CeresClone:1895506 (SEQ ID NO:1011), gi|974776 (SEQ ID NO:1019), gi|5669640 (SEQ ID NO:1020), CeresClone:1390343 (SEQ ID NO:1021), CeresClone:683923 (SEQ ID NO:1023), gi|313029 (SEQ ID NO:1024), CeresClone:1725800 (SEQ ID NO:1025), gi|2808638 (SEQ ID NO:1026), gi|50935375 (SEQ ID NO:1029), CeresClone:1802574 (SEQ ID NO:1031), and gi|549809 (SEQ ID NO:1048).

FIG. 63 is an alignment of the amino acid sequence of Ceres Clone 557009 (SEQ ID NO:1052) with homologous and/or orthologous amino acid sequences gi|92897616 (SEQ ID NO:1053), CeresAnnot:1474923 (SEQ ID NO:1055), and gi|21592849 (SEQ ID NO:1056).

FIG. 64 is an alignment of the amino acid sequence of Ceres Clone 6042 (SEQ ID NO:1064) with homologous and/or orthologous amino acid sequences gi|32401273 (SEQ ID NO:1065), gi|28274828 (SEQ ID NO:1066), CeresClone:1926437 (SEQ ID NO:1068), gi|92878372 (SEQ ID NO:1069), 1446840 (SEQ ID NO:1071), CeresClone:582684 (SEQ ID NO:1072), gi|1208498 (SEQ ID NO:1073), gi|8809571 (SEQ ID NO:1074), CeresClone:1443683 (SEQ ID NO:1075), gi|50911399 (SEQ ID NO:1076), CeresClone:1809375 (SEQ ID NO:1078), and CeresClone:555364 (SEQ ID NO:1079).

FIG. 65 is an alignment of the amino acid sequence of Ceres Clone 6639 (SEQ ID NO:1083) with homologous and/or orthologous amino acid sequences CeresClone:1834027 (SEQ ID NO:1085), 1482536 (SEQ ID NO:1087), CeresClone:463157 (SEQ ID NO:1088), gi|92875402 (SEQ ID NO:1089), 1478227 (SEQ ID NO:1091), gi|21667487 (SEQ ID NO:1092), CeresClone:1755065 (SEQ ID NO:1094), gi|21281083, and gi|9759262.

FIG. 66 is an alignment of the amino acid sequence of Ceres Clone 7774 (SEQ ID NO:1096) with homologous and/or orthologous amino acid sequences 1449565 (SEQ ID NO:1098), gi|92875130 (SEQ ID NO:1099), CeresClone:1728645 (SEQ ID NO:1100), CeresClone:892214 (SEQ ID NO:1101), and gi|50913251 (SEQ ID NO:1102).

FIG. 67 is an alignment of the amino acid sequence of Ceres Clone 8334 (SEQ ID NO:1104) with homologous and/or orthologous amino acid sequences gi|30984532 (SEQ ID NO:1105) and CeresClone:1923641 (SEQ ID NO:1125).

FIG. 68 is an alignment of the amino acid sequence of Ceres Clone 963031 (SEQ ID NO:1131) with homologous and/or orthologous amino acid sequence gi|21554154 (SEQ ID NO:1132).

FIG. 69 is an alignment of the amino acid sequence of Ceres Clone 9804 (SEQ ID NO:1136) with homologous and/or orthologous amino acid sequences CeresClone:1832094 (SEQ ID NO:1143) and CeresClone:1887966 (SEQ ID NO:2065).

FIG. 70 is an alignment of the amino acid sequence of Ceres Clone 99033 (SEQ ID NO:1165) with homologous and/or orthologous amino acid sequences CeresClone:1840223 (SEQ ID NO:1171), CeresAnnot:1514944 (SEQ ID NO:1173), gi|90399248 (SEQ ID NO:1174), CeresClone:1827510 (SEQ ID NO:1176), CeresClone:467336 (SEQ ID NO:1177), CeresClone:1555943 (SEQ ID NO:1180), and gi|9294812 (SEQ ID NO:1181).

FIG. 71 is an alignment of the amino acid sequence of cDNA ID 23389966 (Ceres CLONE ID no. 3929; SEQ ID NO:1185) with homologous and/or orthologous amino acid sequences gi|20197615 (SEQ ID NO:1187), CeresClone:18215 (SEQ ID NO:1188), CeresClone:105261 (SEQ ID NO:1190), CeresClone:24667 (SEQ ID NO:1193), CeresClone:118878 (SEQ ID NO:1195), CeresClone:12459 (SEQ ID NO:1196), and CeresClone:1354021 (SEQ ID NO:1197).

FIG. 72 is an alignment of the amino acid sequence of Ceres Clone 14909 (SEQ ID NO:1211) with homologous and/or orthologous amino acid sequences CeresClone:1561415 (SEQ ID NO:1226), CeresClone:380874 (SEQ ID NO:1227), CeresClone:416460 (SEQ ID NO:1228), CeresClone:631823 (SEQ ID NO:1229), CeresClone:1535974 (SEQ ID NO:1230), CeresClone:1428788 (SEQ ID NO:1231), CeresClone:738726 (SEQ ID NO:1232), CeresClone:276776 (SEQ ID NO:1233), CeresClone:240510 (SEQ ID NO:1234), and CeresClone:529239 (SEQ ID NO:1235).

FIG. 73 is an alignment of the amino acid sequence of Ceres Clone 19340 (SEQ ID NO:1239) with homologous and/or orthologous amino acid sequences CeresClone:573293 (SEQ ID NO:1931), gi|50919203 (SEQ ID NO:1933), CeresClone:230342 (SEQ ID NO:1934), and CeresClone:537080 (SEQ ID NO:1932).

FIG. 74 is an alignment of the amino acid sequence of cDNA ID 23383311 (Ceres CLONE ID no. 21604; SEQ ID NO:1249) with homologous and/or orthologous amino acid sequences CeresClone:824827 (SEQ ID NO:2018), CeresClone:245683 (SEQ ID NO:2015), CeresClone:1283552 (SEQ ID NO:2016), CeresClone:272426 (SEQ ID NO:2017), CeresClone:659723 (SEQ ID NO:2012), CeresClone:1585988 (SEQ ID NO:2014), and CeresClone:953644 (SEQ ID NO:2013).

FIG. 75 is an alignment of the amino acid sequence of Ceres Clone 29637 (SEQ ID NO:1259) with homologous and/or orthologous amino acid sequence gi|34896798 (SEQ ID NO:1946).

FIG. 76 is an alignment of the amino acid sequence of cDNA ID 23384563 (Ceres CLONE ID no. 34414; SEQ ID NO:1267) with homologous and/or orthologous amino acid sequences CeresClone:14909 (SEQ ID NO:1986), CeresClone:1535974 (SEQ ID NO:1991), CeresClone:276776 (SEQ ID NO:1990), CeresClone:240510 (SEQ ID NO:1992), gi|39653273 (SEQ ID NO:1989), CeresClone:33126 (SEQ ID NO:1987), and CeresClone:1338585 (SEQ ID NO:1988).

FIG. 77 is an alignment of the amino acid sequence of Ceres Clone 38311 (SEQ ID NO:1285) with homologous and/or orthologous amino acid sequences CeresClone:19561 (SEQ ID NO:1957), gi|33320073 (SEQ ID NO:1959), CeresClone:597624 (SEQ ID NO:1958), CeresClone:331400 (SEQ ID NO:1961), CeresClone:705041 (SEQ ID NO:1960), and gi|50932645 (SEQ ID NO:1962).

FIG. 78 is an alignment of the amino acid sequence of cDNA ID 23365746 (Ceres CLONE ID no. 109490; SEQ ID NO:1294) with homologous and/or orthologous amino acid sequences CeresClone:475016 (SEQ ID NO:1976), CeresClone:1571937 (SEQ ID NO:1977), and gi|34907424 (SEQ ID NO:1978).

FIG. 79 is an alignment of the amino acid sequence of Ceres Clone 124720 (SEQ ID NO:1302) with homologous and/or orthologous amino acid sequences CeresClone:975672 (SEQ ID NO:1303), CeresClone:1044385 (SEQ ID NO:1304), gi|55419650 (SEQ ID NO:1305), gi|56384582 (SEQ ID NO:1306), gi|57012880 (SEQ ID NO:1307), gi|50929507 (SEQ ID NO:1308), and CeresClone:273307 (SEQ ID NO:1309).

FIG. 80 is an alignment of the amino acid sequence of cDNA ID 23740209 (Ceres CLONE ID no. 208429; SEQ ID NO:1315) with homologous and/or orthologous amino acid sequences CeresClone:471377 (SEQ ID NO:1985), CeresClone:207075 (SEQ ID NO:1982), gi|21554154 (SEQ ID NO:1983), gi|9759080 (SEQ ID NO:1984), CeresClone:617111 (SEQ ID NO:1981), and gi|50940237 (SEQ ID NO:1980).

FIG. 81 is an alignment of the amino acid sequence of Ceres Clone 225321 (SEQ ID NO:1323) with homologous and/or orthologous amino acid sequences gi|1429228 (SEQ ID NO:1945), CeresClone:8364 (SEQ ID NO:1944), CeresClone:530235 (SEQ ID NO:1943), gi|57899877 (SEQ ID NO:1942), CeresClone:1541168 (SEQ ID NO:1939), gi|55585039 (SEQ ID NO:1941), and CeresClone:699465 (SEQ ID NO:1940).

FIG. 82 is an alignment of the amino acid sequence of Ceres Clone 333753 (SEQ ID NO:1333) with homologous and/or orthologous amino acid sequences gi|50726318 (SEQ ID NO:1950) and gi|17017392 (SEQ ID NO:1949).

FIG. 83 is an alignment of the amino acid sequence of Ceres Clone 475689 (SEQ ID NO:1345) with homologous and/or orthologous amino acid sequences gi|50251896 (SEQ ID NO:1970), CeresClone:783774 (SEQ ID NO:1968), gi|37544703 (SEQ ID NO:1969), CeresClone:1151902 (SEQ ID NO:1964), gi|10636051 (SEQ ID NO:1965), gi|22324807 (SEQ ID NO:1963), gi|14270085 (SEQ ID NO:1971), gi|2290532 (SEQ ID NO:1967), and gi|6752886 (SEQ ID NO:1966).

FIG. 84 is an alignment of the amino acid sequence of CeresClone:560948 (SEQ ID NO:1361) with homologous and/or orthologous amino acid sequences Ceres Clone: 945972 (SEQ ID NO:1362), Ceres Clone: 503296 (SEQ ID NO:1367), and CeresClone:1759397 (SEQ ID NO:1369).

FIG. 85 is an alignment of the amino acid sequence of cDNA ID 23402435 (Ceres CLONE ID no. 597624; SEQ ID NO:1371) with homologous and/or orthologous amino acid sequences gi|33320073 (SEQ ID NO:1288) and gi|15810645.

FIG. 86 is an alignment of the amino acid sequence of cDNA ID 23385230 (Ceres CLONE ID no. 108109; SEQ ID NO:1377) with homologous and/or orthologous amino acid sequences CeresClone:354956 (SEQ ID NO:2009), gi|22854970 (SEQ ID NO:2010), gi|22854950 (SEQ ID NO:2011), gi|25405956 (SEQ ID NO:2007), and gi|30694486 (SEQ ID NO:2008).

FIG. 87 is an alignment of the amino acid sequence of Ceres Clone 115924 (SEQ ID NO:1383) with homologous and/or orthologous amino acid sequences CeresClone:894637 (SEQ ID NO:1923), gi|50725048 (SEQ ID NO:1924), and CeresClone:477003 (SEQ ID NO:1922).

FIG. 88 is an alignment of the amino acid sequence of cDNA ID 23449314 (Ceres CLONE ID no. 120302; SEQ ID NO:1395) with homologous and/or orthologous amino acid sequences CeresClone:1459729 (SEQ ID NO:2032), gi|56749359 (SEQ ID NO:2019), gi|1167484 (SEQ ID NO:2027), gi|50726662 (SEQ ID NO:2028), gi|19053 (SEQ ID NO:2029), gi|47680445 (SEQ ID NO:2033), gi|39725415 (SEQ ID NO:2025), gi|31980095 (SEQ ID NO:2026), and gi|13346194 (SEQ ID NO:2023).

FIG. 89 is an alignment of the amino acid sequence of Ceres Clone 12071 (SEQ ID NO:1405) with homologous and/or orthologous amino acid sequences gi|55419652 (SEQ ID NO:1406), gi|1183866 (SEQ ID NO:1407), CeresClone:538817 (SEQ ID NO:1408), gi|30577630 (SEQ ID NO:1409), and gi|62856979 (SEQ ID NO:2059).

FIG. 90 is an alignment of the amino acid sequence of Ceres Clone 12997 (SEQ ID NO:1414) with homologous and/or orthologous amino acid sequence CeresClone:465893 (SEQ ID NO:1415).

FIG. 91 is an alignment of the amino acid sequence of Ceres Clone 14246 (SEQ ID NO:1423) with homologous and/or orthologous amino acid sequences gi|3550485 (SEQ ID NO:1424), CeresClone:1537388 (SEQ ID NO:1425), CeresClone:511197 (SEQ ID NO:1426), gi|50934311 (SEQ ID NO:1929), gi|311952 (SEQ ID NO:1926), and gi|20005 (SEQ ID NO:1927).

FIG. 92 is an alignment of the amino acid sequence of CeresClone:149496 (SEQ ID NO:1436) with homologous and/or orthologous amino acid sequences CeresClone:833872 (SEQ ID NO:1439) and CeresClone:1579587 (SEQ ID NO:1442).

FIG. 93 is an alignment of the amino acid sequence of cDNA ID 23358452 (Ceres CLONE ID no. 16204; SEQ ID NO:1444) with homologous and/or orthologous amino acid sequences CeresClone:873113 (SEQ ID NO:1449), CeresClone:956177 (SEQ ID NO:1450), CeresClone:721511 (SEQ ID NO:1451), CeresClone:641329 (SEQ ID NO:1452), CeresClone:782784 (SEQ ID NO:1453), gi|18645 (SEQ ID NO:1454), gi|1052956 (SEQ ID NO:1455), gi|436424 (SEQ ID NO:1456), gi|2894109 (SEQ ID NO:1457), CeresClone:686294 (SEQ ID NO:1458), gi|50726318 (SEQ ID NO:1459), gi|729737 (SEQ ID NO:1460), gi|729736 (SEQ ID NO:1461), CeresClone:1060767 (SEQ ID NO:1462), and gi|7446231 (SEQ ID NO:1463).

FIG. 94 is an alignment of the amino acid sequence of Ceres Clone 207419 (SEQ ID NO:1465) with homologous and/or orthologous amino acid sequences CeresClone:212775 (SEQ ID NO:1936) and gi|12597770 (SEQ ID NO:1935).

FIG. 95 is an alignment of the amino acid sequence of Ceres Clone 20769 (SEQ ID NO:1469) with homologous and/or orthologous amino acid sequences CeresClone:477718 (SEQ ID NO:1937) and CeresClone:518521 (SEQ ID NO:1938).

FIG. 96 is an alignment of the amino acid sequence of CeresClone:21374 (SEQ ID NO:1475) with homologous and/or orthologous amino acid sequence 1471763 (SEQ ID NO:1477).

FIG. 97 is an alignment of the amino acid sequence of cDNA ID 23369680 (Ceres CLONE ID no. 21863; SEQ ID NO:1481) with homologous and/or orthologous amino acid sequences gi|34902106 (SEQ ID NO:1488), CeresClone:677852 (SEQ ID NO:1490), and CeresClone:637282 (SEQ ID NO:1491).

FIG. 98 is an alignment of the amino acid sequence of cDNA ID 23371050 (Ceres CLONE ID no. 250132; SEQ ID NO:1493) with homologous and/or orthologous amino acid sequences CeresClone:962327 (SEQ ID NO:1494), CeresClone:1101577 (SEQ ID NO:1495), CeresClone:634261 (SEQ ID NO:1496), gi|5031281 (SEQ ID NO:1497), gi|35187687 (SEQ ID NO:1498), gi|34978689 (SEQ ID NO:1499), and gi|34909836 (SEQ ID NO:1500).

FIG. 99 is an alignment of the amino acid sequence of 532H5 (Ceres CLONE ID no. 251466; SEQ ID NO:1504) with homologous and/or orthologous amino acid sequences gi|50253268 (SEQ ID NO:1505), gi|45826359 (SEQ ID NO:1506), gi|45826360 (SEQ ID NO:1507), gi|37993864 (SEQ ID NO:1508), CeresClone:707775 (SEQ ID NO:1509), gi|38257023 (SEQ ID NO:1510), gi|37147896 (SEQ ID NO:1511), gi|41351817 (SEQ ID NO:1512), gi|55824656 (SEQ ID NO:1513), gi|66269671 (SEQ ID NO:1514), gi|33638194 (SEQ ID NO:1515), and gi|21908034 (SEQ ID NO:1516).

FIG. 100 is an alignment of the amino acid sequence of Ceres Clone 25795 (SEQ ID NO:1518) with homologous and/or orthologous amino acid sequence CeresClone:1104601.

FIG. 101 is an alignment of the amino acid sequence of CeresClone:26867 (SEQ ID NO:1526) with homologous and/or orthologous amino acid sequence Annot ID:1486918 (SEQ ID NO:1528).

FIG. 102 is an alignment of the amino acid sequence of cDNA ID 23792467 (Ceres CLONE ID no. 325800; SEQ ID NO:1540) with homologous and/or orthologous amino acid sequences gi|4519671, gi|32470645, CeresClone:677527, CeresClone:537360, and gi|4835766.

FIG. 103 is an alignment of the amino acid sequence of cDNA ID 23377150 (Ceres CLONE ID no. 33333; SEQ ID NO:1552) with homologous and/or orthologous amino acid sequences CeresClone:543289 (SEQ ID NO:2036), gi|30575840 (SEQ ID NO:2034), and gi|22795039 (SEQ ID NO:2035).

FIG. 104 is an alignment of the amino acid sequence of Ceres Clone 333416 (SEQ ID NO:1564) with homologous and/or orthologous amino acid sequences CeresClone:108509 (SEQ ID NO:1947) and CeresClone:764678 (SEQ ID NO:1948).

FIG. 105 is an alignment of the amino acid sequence of ME LINE ME01130 (Ceres CLONE ID no. 34589; SEQ ID NO:1570) with homologous and/or orthologous amino acid sequence CeresClone:975220 (SEQ ID NO:1979).

FIG. 106 is an alignment of the amino acid sequence of Ceres Clone 36272 (SEQ ID NO:1573) with homologous and/or orthologous amino acid sequences CeresClone:573215 (SEQ ID NO:1955), CeresClone:474481 (SEQ ID NO:1956), gi|1922964 (SEQ ID NO:1954), gi|6289057 (SEQ ID NO:1953), CeresClone:1911 (SEQ ID NO:1951), and gi|23505813 (SEQ ID NO:1952).

FIG. 107 is an alignment of the amino acid sequence of cDNA ID 23814706 (Ceres CLONE ID no. 397320; SEQ ID NO:1585) with homologous and/or orthologous amino acid sequences gi|37991859 (SEQ ID NO:2055), CeresClone:327449 (SEQ ID NO:2054), CeresClone:476445 (SEQ ID NO:2053), CeresClone:1066463 (SEQ ID NO:2052), CeresClone:1349 (SEQ ID NO:2046), and CeresClone:1099781 (SEQ ID NO:2051).

FIG. 108 is an alignment of the amino acid sequence of CeresClone:41439 (SEQ ID NO:1595) with homologous and/or orthologous amino acid sequences CeresClone:701379 (SEQ ID NO:1602) and CeresClone:638614 (SEQ ID NO:1604).

FIG. 109 is an alignment of the amino acid sequence of Ceres CLONE ID no. 42530 (SEQ ID NO:1610) with homologous and/or orthologous amino acid sequences CeresClone:30700 (SEQ ID NO:2068), gi|19698881 (SEQ ID NO:2070), gi|25809054 (SEQ ID NO:2083), gi|2119932 (SEQ ID NO:2076), gi|19697 (SEQ ID NO:2071), gi|475216 (SEQ ID NO:2073), and gi|2119933 (SEQ ID NO:2080).

FIG. 110 is an alignment of the amino acid sequence of Ceres Clone 45 (SEQ ID NO:1620) with homologous and/or orthologous amino acid sequences CeresClone:962327 (SEQ ID NO:1621) and CeresClone:1360570 (SEQ ID NO:1622).

FIG. 111 is an alignment of the amino acid sequence of Ceres Clone 560731 (SEQ ID NO:1628) with homologous and/or orthologous amino acid sequences CeresClone:4267 (SEQ ID NO:1972) and CeresClone:1377336 (SEQ ID NO:1973).

FIG. 112 is an alignment of the amino acid sequence of Ceres Clone 6397 (SEQ ID NO:1637) with homologous and/or orthologous amino acid sequences gi|57012876 (SEQ ID NO:1645) and gi|3342211 (SEQ ID NO:1651).

FIG. 113 is an alignment of the amino acid sequence of CeresClone:660003 (SEQ ID NO:1653) with homologous and/or orthologous amino acid sequences CeresClone:763852 (SEQ ID NO:1655) and Annot ID:1508184 (SEQ ID NO:1657).

FIG. 114 is an alignment of the amino acid sequence of CeresClone:681088 (SEQ ID NO:1661) with homologous and/or orthologous amino acid sequence Annot ID:1471330 (SEQ ID NO:1663).

FIG. 115 is an alignment of the amino acid sequence of CeresClone:691319 (SEQ ID NO:1675) with homologous and/or orthologous amino acid sequence CeresClone:1475648 (SEQ ID NO:1676).

FIG. 116 is an alignment of the amino acid sequence of cDNA ID 23380615 (Ceres CLONE ID no. 7559; SEQ ID NO:1681) with homologous and/or orthologous amino acid sequences CeresClone:844350 (SEQ ID NO:1685), gi|52140009 (SEQ ID NO:1686), CeresClone:298172 (SEQ ID NO:1687), gi|52140013 (SEQ ID NO:1688), CeresClone:541062 (SEQ ID NO:1689), gi|52140015 (SEQ ID NO:1690), and gi|52140010 (SEQ ID NO:2006).

FIG. 117 is an alignment of the amino acid sequence of CeresClone:92102 (SEQ ID NO:1692) with homologous and/or orthologous amino acid sequences CeresClone:965028, gi|45642990, gi|40060531, gi|38260618, and CeresClone:548557.

FIG. 118 is an alignment of the amino acid sequence of ME05220 (Ceres CLONE ID no. 968026; SEQ ID NO:1698) with homologous and/or orthologous amino acid sequences CeresClone:596510 (SEQ ID NO:2057) and gi|28466913 (SEQ ID NO:2056).

FIG. 119 is an alignment of the amino acid sequence of cDNA ID 23498685 5109H3 (Ceres ANNOT ID no. 552542; SEQ ID NO:1722) with homologous and/or orthologous amino acid sequences CeresClone:727056 (SEQ ID NO:1996), gi|52077327 (SEQ ID NO:1993), CeresClone:1548279 (SEQ ID NO:1995), and CeresClone:1044645 (SEQ ID NO:1994).

FIG. 120 is an alignment of the amino acid sequence of cDNA ID 23653450 5109C6 (Ceres ANNOT ID no. 574705; SEQ ID NO:1728) with homologous and/or orthologous amino acid sequences gi|50938747 (SEQ ID NO:1729), CeresClone:458156 (SEQ ID NO:1730), and CeresClone:918824 (SEQ ID NO:1731).

FIG. 121 is an alignment of the amino acid sequence of cDNA ID 23522373 5110H5 (Ceres ANNOT ID no. 834509; SEQ ID NO:1735) with homologous and/or orthologous amino acid sequences gi|3608135 (SEQ ID NO:1736), gi|3336903 (SEQ ID NO:1738), CeresClone:545441 (SEQ ID NO:1739), gi|5381313 (SEQ ID NO:1740), gi|3336906 (SEQ ID NO:1741), gi|13775109 (SEQ ID NO:1742), gi|435942 (SEQ ID NO:1743), and CeresClone:287677 (SEQ ID NO:1746).

FIG. 122 is an alignment of the amino acid sequence of cDNA ID 23401690 (Ceres CLONE ID no. 603410; SEQ ID NO:1752) with homologous and/or orthologous amino acid sequences CeresClone:605218 (SEQ ID NO:1753), gi|57012759 (SEQ ID NO:1754), CeresClone:6397 (SEQ ID NO:1755), CeresClone:282666 (SEQ ID NO:1756), gi|32401273 (SEQ ID NO:1757), CeresClone:592713 (SEQ ID NO:1758), gi|3342211 (SEQ ID NO:1759), gi|57012876 (SEQ ID NO:1760), CeresClone:555364 (SEQ ID NO:1761), CeresClone:944101 (SEQ ID NO:1762), CeresClone:569593 (SEQ ID NO:1763), and gi|50927517 (SEQ ID NO:1764).

FIG. 123 is an alignment of the amino acid sequence of cDNA ID 23556617 (Ceres CLONE ID no. 32791; SEQ ID NO:1767) with homologous and/or orthologous amino acid sequences gi|1568513 (SEQ ID NO:1769), gi|20385590 (SEQ ID NO:1770), gi|27763670 (SEQ ID NO:1771), gi|60100358 (SEQ ID NO:1772), gi|48727598 (SEQ ID NO:1774), gi|21955182 (SEQ ID NO:1775), gi|3646326 (SEQ ID NO:1998), CeresClone:1044034 (SEQ ID NO:1999), gi|23194453 (SEQ ID NO:1997), gi|4103342 (SEQ ID NO:2000), gi|42794560 (SEQ ID NO:2003), gi|57157565 (SEQ ID NO:2002), and gi|29467048 (SEQ ID NO:2004).

FIG. 124 is an alignment of the amino acid sequence of CeresClone:541719 (SEQ ID NO:1779) with homologous and/or orthologous amino acid sequence Annot ID:1535677 (SEQ ID NO:1783).

FIG. 125 is an alignment of the amino acid sequence of cDNA ID 23557650 (Ceres CLONE ID no. 8607; SEQ ID NO:1785) with homologous and/or orthologous amino acid sequences CeresClone:1033993 (SEQ ID NO:1786), CeresClone:703180 (SEQ ID NO:1787), CeresClone:560681 (SEQ ID NO:1788), CeresClone:560948 (SEQ ID NO:1790), CeresClone:653656 (SEQ ID NO:1792), gi|50929085 (SEQ ID NO:1794), gi|50912765 (SEQ ID NO:1795), CeresClone:503296 (SEQ ID NO:1796), and CeresClone:486120 (SEQ ID NO:1797).

FIG. 126 is an alignment of the amino acid sequence of CeresClone:519 (SEQ ID NO:1806) with homologous and/or orthologous amino acid sequences CeresClone:951040 (SEQ ID NO:1811), CeresClone:703180 (SEQ ID NO:1814), and 1247092 (SEQ ID NO:1820).

FIG. 127 is an alignment of the amino acid sequence of CeresClone:106887 (SEQ ID NO:1832) with homologous and/or orthologous amino acid sequence 1796871 (SEQ ID NO:1834).

FIG. 128 is an alignment of the amino acid sequence of CeresClone:25793 (SEQ ID NO:1854) with homologous and/or orthologous amino acid sequence CeresClone:1881639 (SEQ ID NO:1856).

FIG. 129 is an alignment of the amino acid sequence of Annot ID:1493072 (SEQ ID NO:1892) with homologous and/or orthologous amino acid sequences gi|39725413 (SEQ ID NO:1894) and gi|71041096 (SEQ ID NO:1895).

FIG. 130 is an alignment of the amino acid sequence of CeresClone:5398 (SEQ ID NO:1897) with homologous and/or orthologous amino acid sequences CeresClone:1836567 (SEQ ID NO:1899), 1458988 (SEQ ID NO:1901), and gi|92899044 (SEQ ID NO:1902).

FIG. 131 is an alignment of the amino acid sequence of cDNA ID 23367406 (Ceres CLONE ID no. 9325; SEQ ID NO:1906) with homologous and/or orthologous amino acid sequences gi|7443216, CeresClone:982579 (SEQ ID NO:2045), gi|11133887 (SEQ ID NO:2041), CeresClone:1139782 (SEQ ID NO:2042), gi|42569485 (SEQ ID NO:2044), gi|21133 (SEQ ID NO:2040), CeresClone:1063835 (SEQ ID NO:2038), CeresClone:1027529 (SEQ ID NO:2039), and CeresClone:142681 (SEQ ID NO:2037).

DETAILED DESCRIPTION

Applicants have identified regulatory proteins (e.g., transcription factors) that are “associated” with regulatory regions (e.g., promoters) of genes encoding enzymes involved in lignin biosynthesis. A regulatory protein and a regulatory region are considered to be “associated” when the regulatory protein is capable of modulating expression, either directly or indirectly, of a nucleic acid operably linked to the regulatory region. For example, a regulatory protein and a regulatory region can be said to be associated when the regulatory protein directly binds to the regulatory region, as in a transcription factor-promoter complex. In some cases, a regulatory protein and regulatory region can be said to be associated when the regulatory protein does not directly bind to the regulatory region. A regulatory protein and a regulatory region can also be said to be associated when the regulatory protein indirectly affects transcription by being a component of a protein complex involved in transcriptional regulation or by noncovalently binding to a protein complex involved in transcriptional regulation. In some cases, a regulatory protein and regulatory region can be said to be associated and indirectly affect transcription when the regulatory protein participates in or is a component of a signal transduction cascade or a proteasome degradation pathway (e.g., of repressors) that results in transcriptional amplification or repression. In some cases, regulatory proteins associate with regulatory regions and indirectly affect expression by, e.g., binding to methylated DNA, unwinding chromatin, or binding to RNA.

Knowledge of associations between regulatory proteins and regulatory regions can be used to create plant cells and plants having modulated levels of expression of a sequence of interest, such as a sequence comprising a coding sequence for an enzyme involved in lignin biosynthesis. For example, plant cells and plants can be created that contain a nucleic acid encoding a regulatory protein that is associated with an endogenous regulatory region of an endogenous gene encoding an enzyme involved in lignin biosynthesis. The regulatory protein can modulate expression of the endogenous gene operably linked to the associated, endogenous regulatory region. In some embodiments, plant cells and plants can be created that contain (1) a nucleic acid encoding a regulatory protein, and (2) a nucleic acid including a regulatory region that is associated with the regulatory protein and that is operably linked to a sequence of interest. Thus, a regulatory protein can modulate expression of any sequence of interest operably linked to an associated regulatory region.

Selective modulation of the expression of a sequence of interest, such as a sequence encoding a polypeptide involved in lignin biosynthesis, can allow biosynthetic pathways, such as the lignin biosynthesis pathway, to be manipulated. In addition, the use of regulatory protein-regulatory region associations in plants can permit selective modulation of the amount or rate of biosynthesis of plant polypeptides, e.g., enzymes involved in lignin biosynthesis, and plant compounds, e.g., lignin monomers and polymers, under a desired environmental condition or in a desired plant developmental pathway.

Polypeptides

The term “polypeptide” as used herein refers to a compound of two or more subunit amino acids, amino acid analogs, or other peptidomimetics, regardless of post-translational modification, e.g., phosphorylation or glycosylation. The subunits may be linked by peptide bonds or other bonds such as, for example, ester or ether bonds. The term “amino acid” refers to natural and/or unnatural or synthetic amino acids, including D/L optical isomers. Full-length proteins, analogs, mutants, and fragments thereof are encompassed by this definition.

The term “isolated” with respect to a polypeptide refers to a polypeptide that has been separated from cellular components that naturally accompany it. Typically, the polypeptide is isolated when it is at least 60%, e.g., 70%, 80%, 90%, 95%, or 99%, by weight, free from polypeptides and naturally occurring organic molecules that are naturally associated with it. In general, an isolated polypeptide will yield a single major band on a reducing and/or non-reducing polyacrylamide gel. Isolated polypeptides can be obtained, for example, by extraction from a natural source (e.g., plant tissue), chemical synthesis, or by recombinant production in a host plant cell. To recombinantly produce a polypeptide, a nucleic acid sequence containing a nucleotide sequence encoding a polypeptide of interest can be ligated into an expression vector and used to transform a bacterial, eukaryotic, or plant host cell, e.g., insect, yeast, mammalian, or plant cells. The expressed polypeptide can be extracted from the host cells and purified using techniques known to those of skill in the art.

Polypeptides described herein include regulatory proteins. Such a regulatory protein typically is effective for modulating expression of a nucleic acid sequence operably linked to an associated regulatory region (e.g., an associated promoter) when expressed in a plant or plant cell. Modulation of expression of a nucleic acid sequence can be either an increase or a decrease in expression of the nucleic acid sequence relative to the average rate or level of expression of the nucleic acid sequence in a control plant. Such polypeptides typically contain at least one domain indicative of regulatory proteins, as described in more detail herein. Regulatory proteins typically have an HMM bit score that is greater than about 25, as described in more detail herein. In some embodiments, regulatory proteins have greater than 30% identity to SEQ ID NOs:96, 106, 119, 134, 149, 165, 178, 221, 339, 357, 361, 374, 381, 417, 432, 438, 445, 461, 465, 490, 504, 520, 526, 529, 548, 555, 566, 585, 590, 601, 614, 638, 652, 661, 671, 680, 686, 689, 695, 698, 703, 707, 730, 737, 744, 760, 781, 793, 808, 816, 838, 852, 865, 885, 900, 914, 938, 964, 980, 994, 1052, 1064, 1083, 1096, 1104, 1131, 1136, 1165, 1185, 1211, 1239, 1249, 1259, 1267, 1285, 1294, 1302, 1315, 1323, 1333, 1345, 1361, 1371, 1377, 1383, 1395, 1405, 1414, 1423, 1436, 1444, 1465, 1469, 1475, 1481, 1493, 1504, 1518, 1526, 1540, 1552, 1564, 1570, 1573, 1585, 1595, 1610, 1620, 1628, 1637, 1653, 1661, 1675, 1681, 1692, 1698, 1722, 1728, 1735, 1752, 1767, 1779, 1785, 1806, 1832, 1854, 1892, 1897, and 1906, as described in more detail herein.

In some embodiments, one or more functional homologs of a reference regulatory protein defined by one or more of the pfam descriptions indicated herein are suitable for use as regulatory proteins. A functional homolog is a polypeptide that has sequence similarity to a reference polypeptide, and that carries out one or more of the biochemical or physiological function(s) of the reference polypeptide. A functional homolog and the reference polypeptide may be natural occurring polypeptides, and the sequence similarity may be due to convergent or divergent evolutionary events. As such, functional homologs are sometimes designated in the literature as homologs, or orthologs, or paralogs. Variants of a naturally occurring functional homolog, such as polypeptides encoded by mutants of a wild type coding sequence, may themselves be functional homologs. Functional homologs can also be created via site-directed mutagenesis of the coding sequence for a regulatory protein, or by combining domains from the coding sequences for different naturally-occurring regulatory proteins (“domain swapping”). The term “functional homolog” is sometimes applied to the nucleic acid that encodes a functionally homologous polypeptide.

Functional homologs can be identified by analysis of nucleotide and polypeptide sequence alignments. For example, performing a query on a database of nucleotide or polypeptide sequences can identify homologs of regulatory proteins. Sequence analysis can involve BLAST, Reciprocal BLAST, or PSI-BLAST analysis of nonredundant databases using a regulatory protein amino acid sequence as the reference sequence. Amino acid sequence is, in some instances, deduced from the nucleotide sequence. Those polypeptides in the database that have greater than 40% sequence identity are candidates for further evaluation for suitability as a regulatory protein. Amino acid sequence similarity allows for conservative amino acid substitutions, such as substitution of one hydrophobic residue for another or substitution of one polar residue for another. If desired, manual inspection of such candidates can be carried out in order to narrow the number of candidates to be further evaluated. Manual inspection can be performed by selecting those candidates that appear to have domains present in regulatory proteins, e.g., conserved functional domains.

Conserved regions can be identified by locating a region within the primary amino acid sequence of a regulatory protein that is a repeated sequence, forms some secondary structure (e.g., helices and beta sheets), establishes positively or negatively charged domains, or represents a protein motif or domain. See, e.g., the Pfam web site describing consensus sequences for a variety of protein motifs and domains on the World Wide Web at sanger.ac.uk/Software/Pfam/ and pfam.janelia.org/. A description of the information included at the Pfam database is described in Sonnhammer et al., Nucl. Acids Res., 26:320-322 (1998); Sonnhammer et al., Proteins, 28:405-420 (1997); and Bateman et al., Nucl. Acids Res., 27:260-262 (1999). Conserved regions also can be determined by aligning sequences of the same or related polypeptides from closely related species. Closely related species preferably are from the same family. In some embodiments, alignment of sequences from two different species is adequate.

Typically, polypeptides that exhibit at least about 40% amino acid sequence identity are useful to identify conserved regions. Conserved regions of related polypeptides exhibit at least 45% amino acid sequence identity (e.g., at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% amino acid sequence identity). In some embodiments, a conserved region exhibits at least 92%, 94%, 96%, 98%, or 99% amino acid sequence identity.

A regulatory protein can have one or more zinc finger domains. Zinc finger domains are found in numerous nucleic acid-binding polypeptides. A zinc finger domain is composed of about 25 to 30 amino acid residues, typically including two conserved cysteine (C) and two conserved histidine (H) residues in a C-2-C-12-H-3-H type motif. The 12 residues separating the second cysteine and the first histidine are mainly polar and basic, implicating this region, in particular, in nucleic acid binding. The zinc finger motif is a small, self-folding domain in which zinc is a crucial component of the tertiary structure. Zinc finger domains bind one atom of zinc in a tetrahedral array to yield a finger-like projection, which interacts with nucleotides in the major groove of a nucleic acid. The zinc atom binds to the conserved cysteine and histidine residues. Zinc fingers have been found to bind to about five base pairs of nucleic acid containing short runs of guanine residues. Zinc fingers can bind to RNA and DNA, and it has been suggested that the zinc finger may thus represent the original nucleic acid binding polypeptide. It has also been suggested that a zinc-centered domain can be used in a polypeptide interaction, e.g., in protein kinase C. Many classes of zinc fingers are characterized according to the number and positions of the histidine and cysteine residues involved in the zinc atom coordination. In the C2H2 class, for example, the first pair of zinc coordinating residues are cysteines, while the second pair are histidines.

In some cases, a regulatory protein can contain a zf-C3HC4 domain characteristic of a C3HC4 type (RING finger) zinc-finger polypeptide. The RING finger is a specialized type of zinc-finger of 40 to 60 residues that binds two atoms of zinc and is reported to be involved in mediating polypeptide-polypeptide interactions. There are two different variants, the C3HC4-type and a C3H2C3-type, which are related despite the different cysteine/histidine pattern. The RING domain has been implicated in diverse biological processes. Ubiquitin-protein ligases (E3s), which determine the substrate specificity for ubiquitylation, have been classified into HECT and RING-finger families. Various RING fingers exhibit binding to E2 ubiquitin-conjugating enzymes. SEQ ID NO:134, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NO:355, SEQ ID NO:405, SEQ ID NO:411, SEQ ID NO:490, SEQ ID NO:529, SEQ ID NO:1165, SEQ ID NO:1481, SEQ ID NO:1628, SEQ ID NO:1858, and SEQ ID NO:1884 set forth the amino acid sequences of DNA clones, identified herein as Ceres ANNOT ID no. 550729 (SEQ ID NO:133), Ceres ANNOT ID no. 829219 (SEQ ID NO:160), Ceres ANNOT ID no. 830468 (SEQ ID NO:162), Ceres CLONE ID no. 110419 (SEQ ID NO:354), Ceres CLONE ID no. 116968 (SEQ ID NO:404), Ceres CLONE ID no. 118756 (SEQ ID NO:410), Ceres CLONE ID no. 156298 (SEQ ID NO:489), Ceres CLONE ID no. 17402 (SEQ ID NO:528), Ceres CLONE ID no. 99033 (SEQ ID NO:1164), Ceres CLONE ID no. 21863 (SEQ ID NO:1480), Ceres CLONE ID no. 560731 (SEQ ID NO:1627), Ceres CLONE ID no. 261272 (SEQ ID NO:1857), and Ceres CLONE ID no. 6163 (SEQ ID NO:1883), respectively, each of which is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a zf-C3HC4 domain).

In some cases, a regulatory protein can contain a zf-C2H2 domain characteristic of C2H2 type zinc finger transcription factor polypeptides. C2H2 zinc-finger family polypeptides play important roles in plant development including floral organogenesis, leaf initiation, lateral shoot initiation, gametogenesis, and seed development. SEQ ID NO:1060, SEQ ID NO:1136, SEQ ID NO:1595, SEQ ID NO:1822, and SEQ ID NO:1870 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 560765 (SEQ ID NO:1059), Ceres CLONE ID no. 9804 (SEQ ID NO:1135), Ceres CLONE ID no. 41439 (SEQ ID NO:1594), Ceres ANNOT ID no. 541941 (SEQ ID NO:1821), and Ceres CLONE ID no. 306139 (SEQ ID NO:1869), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a zf-C2H2 domain).

In some cases, a regulatory protein can contain a zf-CCCH domain characteristic of C-x8-C-x5-C-x3-H type (and similar) zinc finger transcription factor polypeptides. Polypeptides containing zinc finger domains of the C-x8-C-x5-C-x3-H type include zinc finger polypeptides from eukaryotes involved in cell cycle or growth phase-related regulation, e.g., human TIS11B (butyrate response factor 1), a predicted regulatory protein involved in regulating the response to growth factors. Another polypeptide containing this domain is the human splicing factor U2AF 35 kD subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential polypeptide-polypeptide interactions and polypeptide-RNA interactions required for 3′ splice site selection. It has been shown that different zf-CCCH zinc finger polypeptides interact with the 3′ untranslated regions of various mRNAs. SEQ ID NO:1465 and SEQ ID NO:1878 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 207419 (SEQ ID NO:1464) and Ceres CLONE ID no. 558431 (SEQ ID NO:1877), respectively, each of which is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a zf-CCCH domain).

In some cases, a regulatory protein can contain a zf-B_box domain characteristic of a B-box zinc finger polypeptide. The B-box zinc finger domain consists of about 40 amino acids. One or two copies of the B-box domain generally are associated with a ring finger and a coiled coil motif to form the so-called tripartite motif. The B-box domain is found in transcription factors, ribonucleoproteins, and proto-oncoproteins. NMR analysis has revealed that the B-box structure comprises two beta-strands, two helical turns, and three extended loop regions that differ from other zinc binding motifs. SEQ ID NO:370 and SEQ ID NO:1722 set forth the amino acid sequences of DNA clones, referred to herein as Ceres CLONE ID no. 112194 (SEQ ID NO:369) and Ceres Annot ID no. 552542 (SEQ ID NO:1721), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a zf-B_(—)box).

In some cases, a regulatory protein can contain a zf-B_box domain and a CCT motif. The CCT (CONSTANS, CO-like, and TOCl) domain is a highly conserved motif that is rich in basic amino acids. The second half of the CCT motif contains a putative nuclear localization signal and has been shown to be involved in nuclear localization. In addition, the CCT domain may have a role in polypeptide-polypeptide interactions. The CCT domain is found near the C-terminus of plant polypeptides, many of which are involved in light signal transduction. Other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif, or the response regulatory domain, are found in association with the CCT domain. SEQ ID NO:1083 and SEQ ID NO:1377 set forth the amino acid sequences of DNA clones, referred to herein as Ceres CLONE ID no. 6639 (SEQ ID NO:1082) and Ceres CLONE ID no. 108109 (SEQ ID NO:1376), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a zf-B_box and a CCT motif).

In some cases, a regulatory protein can contain a GATA domain characteristic of a GATA zinc finger transcription factor polypeptide. A number of transcription factor polypeptides, including erythroid-specific transcription factor polypeptides and nitrogen regulatory polypeptides, specifically bind the DNA sequence (A/T)GATA(A/G) in the regulatory regions of genes. Such transcription factor polypeptides are therefore termed GATA-binding transcription factors. The interactions occur via highly-conserved zinc finger domains in which the zinc ion is coordinated by four cysteine residues. NMR studies have shown that the core of the zinc finger comprises two irregular anti-parallel beta-sheets and an alpha-helix followed by a long loop to the C-terminal end of the finger. The N-terminus, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA binding domain. The helix and the loop connecting the two beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. This tail is the essential determinant of specific binding. Interactions between the zinc finger and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site. A large number of interactions with the phosphate backbone have also been observed. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contain a single copy of the domain. SEQ ID NO:885 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 41634 (SEQ ID NO:884), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a GATA domain).

In some cases, a regulatory protein containing a GATA domain can also contain a CCT motif described above and a ZIM motif. The ZIM motif is found in a variety of plant transcription factors that contain GATA domains and other motifs. The most conserved amino acids form the pattern TIFF/YXG. The ZIM domain may be involved in DNA binding. SEQ ID NO:1469 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 20769 (SEQ ID NO:1468), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a GATA domain, a CCT motif, and a ZIM motif).

In some cases, a regulatory protein can contain a zf-AN1 domain characteristic of an AN1-like zinc finger transcription factor polypeptide. The zf-AN1 domain was first identified as a zinc finger at the C-terminus of AN1, a ubiquitin-like polypeptide in Xenopus laevis. The following pattern describes the zinc finger: C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C, where X can be any amino acid, and the numbers in brackets indicate the number of residues. SEQ ID NO:1620 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 45 (SEQ ID NO:1619), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a zf-AN1 domain).

In some cases, a regulatory protein can contain a zf-A20 domain. The zf-A20 domain is a zinc finger domain that is found in an A20 (an inhibitor of cell death) polypeptide and is believed to mediate self-association of an A20 polypeptide. These zinc finger domains also mediate IL-1-induced NF-kappa B activation. SEQ ID NO:1493 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 250132 (SEQ ID NO:1492), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a zf-A20 domain).

In some cases, a regulatory protein can have a zf-AN1 domain described above and a zf-A20 domain described above. SEQ ID NO:445 sets forth the amino acid sequence of a DNA clone, referred to herein as Ceres CLONE ID no. 14203 (SEQ ID NO:444), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a zf-AN1 domain and a zf-A20 domain).

In some cases, a regulatory protein can contain a zf-DHHC domain. The DHHC zinc finger domain, also known as NEW1, is predicted to be a zinc binding domain involved in polypeptide-polypeptide or polypeptide-DNA interactions, and palmitoyltransferase activity. SEQ ID NO:816 and SEQ ID NO:1239 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 38360 (SEQ ID NO:815) and Ceres CLONE ID no. 19340 (SEQ ID NO:1238), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a zf-DHHC domain).

In some cases, a regulatory protein can contain a zf-D of domain characteristic of a D of domain zinc finger transcription factor polypeptide. D of (DNA binding with one finger) domain polypeptides are plant-specific transcription factor polypeptides having a highly conserved DNA binding domain. A D of domain is a zinc finger DNA binding domain that resembles the Cys2 zinc finger, although it has a longer putative loop containing an extra Cys residue that is conserved. AOBP, a DNA binding polypeptide in pumpkin (Cucurbita maxima), contains a 52 amino acid D of domain, which is highly conserved in several DNA binding polypeptides of higher plants. SEQ ID NO:374 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 113639 (SEQ ID NO:373), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a zf-D of domain).

In some cases, a regulatory protein can contain a zf-U1 domain characteristic of U1 zinc finger polypeptides. The zf-U1 domain is found in several U1 small nuclear ribonucleoprotein C (U1-C) polypeptides. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5′ splice site at early stages of spliceosome assembly. Recruitment of U1 snRNP to a class of weak 5′ splice sites is promoted by binding of a TIA-1 polypeptide to uridine-rich sequences immediately downstream from the 5′ splice site. Binding of a TIA-1 polypeptide in the vicinity of a 5′ splice site is thought to help stabilize U1 snRNP via a direct interaction with a U1-C polypeptide. It is likely that the zf-U1 domain is a zinc-binding motif. SEQ ID NO:852 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 39855 (SEQ ID NO:851), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a zf-U1 domain).

In some cases, a regulatory protein can contain a zf-MYND, or MYND finger, domain. The MYND (myeloid, Nervy, and DEAF-1) domain is present in a group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants. The MYND domain consists of a cluster of invariantly spaced cysteine and histidine residues that form a potential zinc-binding motif. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in polypeptide-polypeptide interactions. The MYND domain of ETO/MTG8 interacts directly with the N—CoR and SMRT co-repressors. The MYND motif in mammalian polypeptides appears to constitute a polypeptide-polypeptide interaction domain that functions as a co-repressor-recruiting interface. SEQ ID NO:106 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 548715 (SEQ ID NO:105), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a zf-MYND domain).

In some cases, a regulatory protein can contain a zf-RanBP domain characteristic of zinc finger domains in Ran binding polypeptides. Ran is an evolutionary conserved member of the Ras superfamily that regulates receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358 kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear polypeptide import. RanBP2 contains multiple zinc fingers that mediate binding to RanGDP. SEQ ID NO:1826 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 566835 (SEQ ID NO:1825), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a zf-RanBP domain).

In some cases, a regulatory protein can contain a zf-CCHC domain characteristic of a zinc knuckle polypeptide. The zinc knuckle is a zinc binding motif with the sequence CX2CX4HX4C, where X can be any amino acid. The motifs are common to the nucleocapsid polypeptides of retroviruses, and the prototype structure is from HIV. The zinc knuckle family also contains members involved in eukaryotic gene regulation. A zinc knuckle is found in eukaryotic polypeptides involved in RNA binding or single strand DNA binding. SEQ ID NO:1828 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 841947 (SEQ ID NO:1827), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a zf-CCHC domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:134, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NO:355, SEQ ID NO:405, SEQ ID NO:411, SEQ ID NO:490, SEQ ID NO:529, SEQ ID NO:1165, SEQ ID NO:1481, SEQ ID NO:1628, SEQ ID NO:1858, SEQ ID NO:1884, SEQ ID NO:1060, SEQ ID NO:1136, SEQ ID NO:1595, SEQ ID NO:1822, SEQ ID NO:1870, SEQ ID NO:1465, SEQ ID NO:1878, SEQ ID NO:370, SEQ ID NO:1722, SEQ ID NO:1083, SEQ ID NO:1377, SEQ ID NO:885, SEQ ID NO:1469, SEQ ID NO:1620, SEQ ID NO:1493, SEQ ID NO:445, SEQ ID NO:816, SEQ ID NO:1239, SEQ ID NO:374, SEQ ID NO:852, SEQ ID NO:106, SEQ ID NO:1826, or SEQ ID NO:1828. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:134, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NO:355, SEQ ID NO:405, SEQ ID NO:411, SEQ ID NO:490, SEQ ID NO:529, SEQ ID NO:1165, SEQ ID NO:1481, SEQ ID NO:1628, SEQ ID NO:1858, SEQ ID NO:1884, SEQ ID NO:1060, SEQ ID NO:1136, SEQ ID NO:1595, SEQ ID NO:1822, SEQ ID NO:1870, SEQ ID NO:1465, SEQ ID NO:1878, SEQ ID NO:370, SEQ ID NO:1722, SEQ ID NO:1083, SEQ ID NO:1377, SEQ ID NO:885, SEQ ID NO:1469, SEQ ID NO:1620, SEQ ID NO:1493, SEQ ID NO:445, SEQ ID NO:816, SEQ ID NO:1239, SEQ ID NO:374, SEQ ID NO:852, SEQ ID NO:106, SEQ ID NO:1826, or SEQ ID NO:1828. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:134, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NO:355, SEQ ID NO:405, SEQ ID NO:411, SEQ ID NO:490, SEQ ID NO:529, SEQ ID NO:1165, SEQ ID NO:1481, SEQ ID NO:1628, SEQ ID NO:1858, SEQ ID NO:1884, SEQ ID NO:1060, SEQ ID NO:1136, SEQ ID NO:1595, SEQ ID NO:1822, SEQ ID NO:1870, SEQ ID NO:1465, SEQ ID NO:1878, SEQ ID NO:370, SEQ ID NO:1722, SEQ ID NO:1083, SEQ ID NO:1377, SEQ ID NO:885, SEQ ID NO:1469, SEQ ID NO:1620, SEQ ID NO:1493, SEQ ID NO:445, SEQ ID NO:816, SEQ ID NO:1239, SEQ ID NO:374, SEQ ID NO:852, SEQ ID NO:106, SEQ ID NO:1826, or SEQ ID NO:1828.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:134, SEQ ID NO:490, SEQ ID NO:529, SEQ ID NO:1165, SEQ ID NO:1481, SEQ ID NO:1628, SEQ ID NO:1136, SEQ ID NO:1595, SEQ ID NO:1465, SEQ ID NO:1722, SEQ ID NO:1083, SEQ ID NO:1377, SEQ ID NO:885, SEQ ID NO:1469, SEQ ID NO:1620, SEQ ID NO:1493, SEQ ID NO:445, SEQ ID NO:816, SEQ ID NO:1239, SEQ ID NO:374, SEQ ID NO:852, and SEQ ID NO:106 are provided in FIG. 4, FIG. 21, FIG. 25, FIG. 70, FIG. 97, FIG. 111, FIG. 69, FIG. 108, FIG. 94, FIG. 119, FIG. 65, FIG. 86, FIG. 56, FIG. 95, FIG. 110, FIG. 98, FIG. 18, FIG. 51, FIG. 73, FIG. 13, FIG. 54, and FIG. 2, respectively.

For example, the alignment in FIG. 4 provides the amino acid sequences of Annot ID 550729 (SEQ ID NO:134), gi|20340241 (SEQ ID NO:136), CeresClone:473509 (SEQ ID NO:137), CeresAnnot:1525600 (SEQ ID NO:139), CeresClone:1922929 (SEQ ID NO:141), gi|76446335 (SEQ ID NO:146), and gi|37901055 (SEQ ID NO:147). Other homologs and/or orthologs of SEQ ID NO:134 include Public GI no. 15228108 (SEQ ID NO:135), Ceres CLONE ID no. 1841236 (SEQ ID NO:143), and Ceres CLONE ID no. 1931361 (SEQ ID NO:145).

The alignment in FIG. 21 provides the amino acid sequences of Ceres Clone 156298 (SEQ ID NO:490), CeresAnnot:1512948 (SEQ ID NO:492), CeresClone:659211 (SEQ ID NO:497), gi|92877546 (SEQ ID NO:498), CeresClone:1831324 (SEQ ID NO:501), and CeresClone:398632 (SEQ ID NO:502). Other homologs and/or orthologs of SEQ ID NO:490 include Ceres ANNOT ID no. 1459679 (SEQ ID NO:494), Ceres ANNOT ID no. 1463114 (SEQ ID NO:496), Ceres CLONE ID no. 1662905 (SEQ ID NO:499), Ceres ANNOT ID no. 6094234 (SEQ ID NO:2326), and Ceres ANNOT ID no. 6108173 (SEQ ID NO:2340).

The alignment in FIG. 25 provides the amino acid sequences of Ceres Clone 17402 (SEQ ID NO:529), CeresClone:1432566 (SEQ ID NO:530), CeresClone:1500962 (SEQ ID NO:531), CeresClone:1387733 (SEQ ID NO:532), CeresClone:1408748 (SEQ ID NO:533), CeresClone:1834915 (SEQ ID NO:535), CeresClone:1841007 (SEQ ID NO:537), CeresClone:1836048 (SEQ ID NO:539), CeresAnnot:1541305 (SEQ ID NO:541), CeresAnnot:1487895 (SEQ ID NO:543), CeresAnnot:1510353 (SEQ ID NO:545), and gi|68299223 (SEQ ID NO:546). Other homologs and/or orthologs of SEQ ID NO:529 include gi|30794130 (SEQ ID NO:1921) and Ceres ANNOT ID no. 6039428 (SEQ ID NO:2262).

The alignment in FIG. 70 provides the amino acid sequences of Ceres Clone 99033 (SEQ ID NO:1165), CeresClone:1840223 (SEQ ID NO:1171), CeresAnnot:1514944 (SEQ ID NO:1173), gi|90399248 (SEQ ID NO:1174), CeresClone:1827510 (SEQ ID NO:1176), CeresClone:467336 (SEQ ID NO:1177), CeresClone:1555943 (SEQ ID NO:1180), and gi|9294812 (SEQ ID NO:1181). Other homologs and/or orthologs of SEQ ID NO:1165 include Public GI no. 79331357 (SEQ ID NO:1166), Public GI no. 21618121 (SEQ ID NO:1167), Ceres CLONE ID no. 9763 (SEQ ID NO:1168), Public GI no. 20466304 (SEQ ID NO:1169), Ceres CLONE ID no. 481884 (SEQ ID NO:1178), Public GI no. 22165059 (SEQ ID NO:1179), Ceres ANNOT ID no. 6086887 (SEQ ID NO:2316), Ceres ANNOT ID no. 6094234 (SEQ ID NO:2328), and Ceres ANNOT ID no. 6106161 (SEQ ID NO:2336).

The alignment in FIG. 97 provides the amino acid sequences of cDNA ID 23369680 (Ceres CLONE ID no. 21863; SEQ ID NO:1481), gi|34902106 (SEQ ID NO:1488), CeresClone:677852 (SEQ ID NO:1490), and CeresClone:637282 (SEQ ID NO:1491). Other homologs and/or orthologs of SEQ ID NO:1481 include Ceres ANNOT ID no. 1464854 (SEQ ID NO:1483), Ceres ANNOT ID no. 1511378 (SEQ ID NO:1485), Ceres ANNOT ID no. 1454043 (SEQ ID NO:1487), and SEQ ID NO:1489.

The alignment in FIG. 111 provides the amino acid sequences of Ceres Clone 560731 (SEQ ID NO:1628), CeresClone:4267 (SEQ ID NO:1972) and CeresClone:1377336 (SEQ ID NO:1973). Other homologs and/or orthologs of SEQ ID NO:1628 include Ceres GDNA ANNOT ID no. 1506045 (SEQ ID NO:1630) and Ceres GDNA ANNOT ID no. 1495397 (SEQ ID NO:1632).

The alignment in FIG. 69 provides the amino acid sequences of Ceres Clone 9804 (SEQ ID NO:1136), CeresClone:1832094 (SEQ ID NO:1143) and CeresClone:1887966 (SEQ ID NO:2065). Other homologs and/or orthologs of SEQ ID NO:1136 include Ceres CLONE ID no. 1303137 (SEQ ID NO:1137), Ceres CLONE ID no. 1832735 (SEQ ID NO:1139), Public GI no. 29028906 (SEQ ID NO:1140), Public GI no. 4038045 (SEQ ID NO:1141), Ceres CLONE ID no. 624726 (SEQ ID NO:1144), Public GI no. 19698935 (SEQ ID NO:1145), Public GI no. 15810271 (SEQ ID NO:1146), Ceres CLONE ID no. 1551497 (SEQ ID NO:1147), Ceres ANNOT ID no. 1516953 (SEQ ID NO:1149), Public GI no. 7527719 (SEQ ID NO:1150), Public GI no. 45935057 (SEQ ID NO:1151), Ceres CLONE ID no. 1167848 (SEQ ID NO:1152), Public GI no. 51965086 (SEQ ID NO:1153), Public GI no. 55418542 (SEQ ID NO:1154), Ceres ANNOT ID no. 1463658 (SEQ ID NO:1156), Public GI no. 22136762 (SEQ ID NO:1157), Ceres CLONE ID no. 1877855 (SEQ ID NO:1159), Ceres CLONE ID no. 1940423 (SEQ ID NO:1161), Ceres CLONE ID no. 1887966 (SEQ ID NO:2145), and Ceres ANNOT ID no. 6032020 (SEQ ID NO:2250).

The alignment in FIG. 108 provides the amino acid sequences of CeresClone:41439 (SEQ ID NO:1595), CeresClone:701379 (SEQ ID NO:1602) and CeresClone:638614 (SEQ ID NO:1604). Other homologs and/or orthologs of SEQ ID NO:1595 include Public GI no. 7228329 (SEQ ID NO:1596), Public GI no. 2981169 (SEQ ID NO:1597), Public GI no. 55734108 (SEQ ID NO:1598), Public GI no. 439493 (SEQ ID NO:1599), Public GI no. 7488707 (SEQ ID NO:1600), Public GI no. 33771374 (SEQ ID NO:1601), Public GI no. 2058504 (SEQ ID NO:1603), Public GI no. 33331578 (SEQ ID NO:1605), Public GI no. 4666360 (SEQ ID NO:1606), Public GI no. 28849865 (SEQ ID NO:1607), and Public GI no. 2058506 (SEQ ID NO:1608).

The alignment in FIG. 94 provides the amino acid sequences of Ceres Clone 207419 (SEQ ID NO:1465), CeresClone:212775 (SEQ ID NO:1936) and gi|12597770 (SEQ ID NO:1935). Other homologs and/or orthologs of SEQ ID NO:1465 include Ceres ANNOT ID no. 1517208 (SEQ ID NO:1467) and Ceres ANNOT ID no. 6042650 (SEQ ID NO:2274).

The alignment in FIG. 119 provides the amino acid sequences of cDNA ID 23498685 5109H3 (Ceres ANNOT ID no. 552542; SEQ ID NO:1722), CeresClone:727056 (SEQ ID NO:1996), gi|52077327 (SEQ ID NO:1993), CeresClone:1548279 (SEQ ID NO:1995), and CeresClone:1044645 (SEQ ID NO:1994). Other homologs and/or orthologs of SEQ ID NO:1722 include Ceres ANNOT ID no. 1514007 (SEQ ID NO:1724) and Ceres ANNOT ID no. 1460742 (SEQ ID NO:1726).

The alignment in FIG. 65 provides the amino acid sequences of Ceres Clone 6639 (SEQ ID NO:1083), CeresClone:1834027 (SEQ ID NO:1085), 1482536 (SEQ ID NO:1087), CeresClone:463157 (SEQ ID NO:1088), gi|92875402 (SEQ ID NO:1089), 1478227 (SEQ ID NO:1091), gi|21667487 (SEQ ID NO:1092), CeresClone:1755065 (SEQ ID NO:1094), gi|21281083, and gi|9759262.

The alignment in FIG. 86 provides the amino acid sequences of cDNA ID 23385230 (Ceres CLONE ID no. 108109; SEQ ID NO:1377), CeresClone:354956 (SEQ ID NO:2009), gi|22854970 (SEQ ID NO:2010), gi|22854950 (SEQ ID NO:2011), gi|25405956 (SEQ ID NO:2007), and gi|30694486 (SEQ ID NO:2008). Other homologs and/or orthologs of SEQ ID NO:1377 include Ceres ANNOT ID no. 1469082 (SEQ ID NO:1379) and Ceres ANNOT ID no. 1522474 (SEQ ID NO:1381).

The alignment in FIG. 56 provides the amino acid sequences of Ceres Clone 41634 (SEQ ID NO:885), CeresClone:1360604 (SEQ ID NO:887), CeresClone:1844070 (SEQ ID NO:890), and CeresAnnot:1457905 (SEQ ID NO:892). Other homologs and/or orthologs of SEQ ID NO:885 include Public GI no. 4678312 (SEQ ID NO:886), Ceres CLONE ID no. 1380534 (SEQ ID NO:888), Ceres ANNOT ID no. 1465103 (SEQ ID NO:894), and Ceres CLONE ID no. 1919992 (SEQ ID NO:896).

The alignment in FIG. 95 provides the amino acid sequences of Ceres Clone 20769 (SEQ ID NO:1469), CeresClone:477718 (SEQ ID NO:1937) and CeresClone:518521 (SEQ ID NO:1938). Other homologs and/or orthologs of SEQ ID NO:1469 include Ceres ANNOT ID no. 1443644 (SEQ ID NO:1471) and Ceres ANNOT ID no. 6020292 (SEQ ID NO:2220).

The alignment in FIG. 110 provides the amino acid sequences of Ceres Clone 45 (SEQ ID NO:1620), CeresClone:962327 (SEQ ID NO:1621) and CeresClone:1360570 (SEQ ID NO:1622). Other homologs and/or orthologs of SEQ ID NO:1620 include Ceres ANNOT ID no. 1447323 (SEQ ID NO:1624) and Ceres ANNOT ID no. 1491680 (SEQ ID NO:1626).

The alignment in FIG. 98 provides the amino acid sequences of cDNA ID 23371050 (Ceres CLONE ID no. 250132; SEQ ID NO:1493), CeresClone:962327 (SEQ ID NO:1494), CeresClone:1101577 (SEQ ID NO:1495), CeresClone:634261 (SEQ ID NO:1496), gi|5031281 (SEQ ID NO:1497), gi|35187687 (SEQ ID NO:1498), gi|34978689 (SEQ ID NO:1499), and gi|34909836 (SEQ ID NO:1500). Other homologs and/or orthologs of SEQ ID NO:1493 include Ceres ANNOT ID no. 1527653 (SEQ ID NO:1502).

The alignment in FIG. 18 provides the amino acid sequences of Ceres Clone 14203 (SEQ ID NO:445), CeresClone:1021029 (SEQ ID NO:446), CeresClone:974951 (SEQ ID NO:447), 1460527 (SEQ ID NO:449), CeresClone:1853189 (SEQ ID NO:451), gi|92896423 (SEQ ID NO:452), CeresClone:1853430 (SEQ ID NO:454), CeresClone:1734621 (SEQ ID NO:455), gi|50909195 (SEQ ID NO:456), gi|66271037 (SEQ ID NO:457), and 1450673 (SEQ ID NO:459). Other homologs and/or orthologs of SEQ ID NO:445 include Ceres ANNOT ID no. 6063956 (SEQ ID NO:2286).

The alignment in FIG. 51 provides the amino acid sequences of Ceres Clone 38360 (SEQ ID NO:816), gi|108711626 (SEQ ID NO:817), CeresClone:573293 (SEQ ID NO:818), CeresClone:1825572 (SEQ ID NO:820), 1524357 (SEQ ID NO:822), CeresClone:1819666 (SEQ ID NO:824), gi|50919203 (SEQ ID NO:825), CeresClone:230342 (SEQ ID NO:826), CeresClone:1850953 (SEQ ID NO:828), 1470949 (SEQ ID NO:830), and gi|92897066 (SEQ ID NO:831).

The alignment in FIG. 73 provides the amino acid sequences of Ceres Clone 19340 (SEQ ID NO:1239), CeresClone:573293 (SEQ ID NO:1931), gi|50919203 (SEQ ID NO:1933), CeresClone:230342 (SEQ ID NO:1934), and CeresClone:537080 (SEQ ID NO:1932). Other homologs and/or orthologs of SEQ ID NO:1239 include Ceres ANNOT ID no. 1524357 (SEQ ID NO:1241), Ceres ANNOT ID no. 1497053 (SEQ ID NO:1243), Ceres ANNOT ID no. 1500296 (SEQ ID NO:1245), and Ceres CLONE ID no. 1819666 (SEQ ID NO:1247).

The alignment in FIG. 13 provides the amino acid sequences of CeresClone:113639 (SEQ ID NO:374), CeresClone:562894 (SEQ ID NO:375) and CeresAnnot:1503065 (SEQ ID NO:377).

The alignment in FIG. 54 provides the amino acid sequences of Ceres Clone 39855 (SEQ ID NO:852), CeresClone:1065335 (SEQ ID NO:853), CeresClone:1793747 (SEQ ID NO:855), CeresClone:788576 (SEQ ID NO:856), CeresClone:465010 (SEQ ID NO:857), CeresClone:1832492 (SEQ ID NO:859), CeresClone:1801885 (SEQ ID NO:861), CeresClone:1060804 (SEQ ID NO:862), gi|50948587 (SEQ ID NO:863), and gi|20259185 (SEQ ID NO:2066).

The alignment in FIG. 2 provides the amino acid sequences of Annot ID 548715 (SEQ ID NO:106), CeresAnnot:1447956 (SEQ ID NO:108), CeresClone:1923054 (SEQ ID NO:110), CeresClone:1051305 (SEQ ID NO:111), gi|50923813 (SEQ ID NO:112), CeresClone:1746793 (SEQ ID NO:114), CeresClone:843382 (SEQ ID NO:115), and CeresClone:1540519 (SEQ ID NO:116). Other homologs and/or orthologs of SEQ ID NO:106 include Ceres CLONE ID no. 488960 (SEQ ID NO:117).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:370 include Ceres CLONE ID no. 1768915 (SEQ ID NO:2121) and Ceres ANNOT ID no. 6025808 (SEQ ID NO:2230).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1858 include Ceres ANNOT ID no. 6007065 (SEQ ID NO:2168) and Ceres ANNOT ID no. 6007067 (SEQ ID NO:2170).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:411 include Ceres ANNOT ID no. 6009287 (SEQ ID NO:2172).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:135-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:530-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NO:1921, SEQ ID NOs:1166-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NO:1630, SEQ ID NO:1632, SEQ ID NOs:1972-1973, SEQ ID NO:1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:2065, SEQ ID NOs:1596-1608, SEQ ID NO:1467, SEQ ID NOs:1935-1936, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1993-1996, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, gi|21281083, gi|9759262, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NOs:2007-2011, SEQ ID NOs:886-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:1471, SEQ ID NOs:1937-1938, SEQ ID NOs:1621-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NOs:1494-1500, SEQ ID NO:1502, SEQ ID NOs:446-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:817-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NOs:1931-1934, SEQ ID NO:375, SEQ ID NO:377, SEQ ID NO:853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NO:2066, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NO:2121, SEQ ID NO:2145, SEQ ID NO:2168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2220, SEQ ID NO:2230, SEQ ID NO:2250, SEQ ID NO:2262, SEQ ID NO:2274, SEQ ID NO:2286, SEQ ID NO:2316, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2336, or SEQ ID NO:2340.

A regulatory protein can contain an AP2 domain characteristic of polypeptides belonging to the AP2/EREBP family of plant transcription factor polypeptides. AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) are prototypic members of a family of transcription factors unique to plants, whose distinguishing characteristic is that they contain the so-called AP2 DNA binding domain. AP2/EREBP genes form a large multigene family encoding polypeptides that play a variety of roles throughout the plant life cycle: from being key regulators of several developmental processes, such as floral organ identity determination and control of leaf epidermal cell identity, to forming part of the mechanisms used by plants to respond to various types of biotic and environmental stress. SEQ ID NO:379, SEQ ID NO:583, SEQ ID NO:680, SEQ ID NO:1052, SEQ ID NO:1062, SEQ ID NO:1064, SEQ ID NO:1081, SEQ ID NO:1183, SEQ ID NO:1302, SEQ ID NO:1504, SEQ ID NO:1526, SEQ ID NO:1637, SEQ ID NO:1661, SEQ ID NO:1675, SEQ ID NO:1692, SEQ ID NO:1752, SEQ ID NO:1850, SEQ ID NO:1882, and SEQ ID NO:1886 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 115358 (SEQ ID NO:378), Ceres CLONE ID no. 222885 (SEQ ID NO:582), Ceres CLONE ID no. 31044 (SEQ ID NO:679), Ceres CLONE ID no. 557009 (SEQ ID NO:1051), Ceres CLONE ID no. 560961 (SEQ ID NO:1061), Ceres CLONE ID no. 6042 (SEQ ID NO:1063), Ceres CLONE ID no. 626054 (SEQ ID NO:1080), Ceres CLONE ID no. 99612 (SEQ ID NO:1182), Ceres CLONE ID no. 124720 (SEQ ID NO:1301), Ceres CLONE ID no. 251466 (SEQ ID NO:1503), Ceres CLONE ID no. 26867 (SEQ ID NO:1525), Ceres CLONE ID no. 6397 (SEQ ID NO:1636), Ceres CLONE ID no. 681088 (SEQ ID NO:1660), Ceres CLONE ID no. 691319 (SEQ ID NO:1674), Ceres CLONE ID no. 92102 (SEQ ID NO:1691), Ceres CLONE ID no. 603410 (SEQ ID NO:1751), Ceres CLONE ID no. 231890 (SEQ ID NO:1849), Ceres CLONE ID no. 605218 (SEQ ID NO:1881), and Ceres CLONE ID no. 625035 (SEQ ID NO:1885), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an AP2 domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:379, SEQ ID NO:583, SEQ ID NO:680, SEQ ID NO:1052, SEQ ID NO:1062, SEQ ID NO:1064, SEQ ID NO:1081, SEQ ID NO:1183, SEQ ID NO:1302, SEQ ID NO:1504, SEQ ID NO:1526, SEQ ID NO:1637, SEQ ID NO:1661, SEQ ID NO:1675, SEQ ID NO:1692, SEQ ID NO:1752, SEQ ID NO:1850, SEQ ID NO:1882, or SEQ ID NO:1886. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:379, SEQ ID NO:583, SEQ ID NO:680, SEQ ID NO:1052, SEQ ID NO:1062, SEQ ID NO:1064, SEQ ID NO:1081, SEQ ID NO:1183, SEQ ID NO:1302, SEQ ID NO:1504, SEQ ID NO:1526, SEQ ID NO:1637, SEQ ID NO:1661, SEQ ID NO:1675, SEQ ID NO:1692, SEQ ID NO:1752, SEQ ID NO:1850, SEQ ID NO:1882, or SEQ ID NO:1886. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:379, SEQ ID NO:583, SEQ ID NO:680, SEQ ID NO:1052, SEQ ID NO:1062, SEQ ID NO:1064, SEQ ID NO:1081, SEQ ID NO:1183, SEQ ID NO:1302, SEQ ID NO:1504, SEQ ID NO:1526, SEQ ID NO:1637, SEQ ID NO:1661, SEQ ID NO:1675, SEQ ID NO:1692, SEQ ID NO:1752, SEQ ID NO:1850, SEQ ID NO:1882, or SEQ ID NO:1886.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:680, SEQ ID NO:1052, SEQ ID NO:1064, SEQ ID NO:1302, SEQ ID NO:1504, SEQ ID NO:1526, SEQ ID NO:1637, SEQ ID NO:1661, SEQ ID NO:1675, SEQ ID NO:1692, and SEQ ID NO:1752 are provided in FIG. 37, FIG. 63, FIG. 64, FIG. 79, FIG. 99, FIG. 101, FIG. 112, FIG. 114, FIG. 115, FIG. 117, and FIG. 122, respectively.

For example, the alignment in FIG. 37 provides the amino acid sequences of Ceres Clone 31044 (SEQ ID NO:680), 1496976 (SEQ ID NO:682), and 1444027 (SEQ ID NO:684). Other homologs and/or orthologs of SEQ ID NO:680 include Ceres CLONE ID no. 902699 (SEQ ID NO:1529), Ceres CLONE ID no. 709819 (SEQ ID NO:1530), Public GI no. 37536842 (SEQ ID NO:1531), Public GI no. 21908034 (SEQ ID NO:1532), Public GI no. 25990951 (SEQ ID NO:1533), SEQ ID NO:1534, Ceres ANNOT ID no. 1486207 (SEQ ID NO:1536), Ceres ANNOT ID no. 1496976 (SEQ ID NO:1538), Ceres ANNOT ID no. 6017518 (SEQ ID NO:2214), Ceres ANNOT ID no. 6017519 (SEQ ID NO:2216), and Ceres ANNOT ID no. 6026758 (SEQ ID NO:2234).

The alignment in FIG. 63 provides the amino acid sequences of Ceres Clone 557009 (SEQ ID NO:1052), gi|92897616 (SEQ ID NO:1053), CeresAnnot:1474923 (SEQ ID NO:1055), and gi|21592849 (SEQ ID NO:1056). Other homologs and/or orthologs of SEQ ID NO:1052 include Ceres ANNOT ID no. 6005736 (SEQ ID NO:2162).

The alignment in FIG. 64 provides the amino acid sequences of Ceres Clone 6042 (SEQ ID NO:1064), gi|32401273 (SEQ ID NO:1065), gi|28274828 (SEQ ID NO:1066), CeresClone:1926437 (SEQ ID NO:1068), gi|92878372 (SEQ ID NO:1069), 1446840 (SEQ ID NO:1071), CeresClone:582684 (SEQ ID NO:1072), gi|1208498 (SEQ ID NO:1073), gi|8809571 (SEQ ID NO:1074), CeresClone:1443683 (SEQ ID NO:1075), gi|50911399 (SEQ ID NO:1076), CeresClone:1809375 (SEQ ID NO:1078), and CeresClone:555364 (SEQ ID NO:1079). Other homologs and/or orthologs of SEQ ID NO:1064 include Ceres ANNOT ID no. 6079953 (SEQ ID NO:2308).

The alignment in FIG. 79 provides the amino acid sequences of Ceres Clone 124720 (SEQ ID NO:1302), CeresClone:975672 (SEQ ID NO:1303), CeresClone:1044385 (SEQ ID NO:1304), gi|55419650 (SEQ ID NO:1305), gi|56384582 (SEQ ID NO:1306), gi|57012880 (SEQ ID NO:1307), gi|50929507 (SEQ ID NO:1308), and CeresClone:273307 (SEQ ID NO:1309). Other homologs and/or orthologs of SEQ ID NO:1302 include Ceres ANNOT ID no. 1441430 (SEQ ID NO:1311), Ceres CLONE ID no. 1761125 (SEQ ID NO:1313), and Ceres ANNOT ID no. 6111686 (SEQ ID NO:2344).

The alignment in FIG. 99 provides the amino acid sequences of 532H5 (Ceres CLONE ID no. 251466; SEQ ID NO:1504), gi|50253268 (SEQ ID NO:1505), gi|45826359 (SEQ ID NO:1506), gi|45826360 (SEQ ID NO:1507), gi|37993864 (SEQ ID NO:1508), CeresClone:707775 (SEQ ID NO:1509), gi|38257023 (SEQ ID NO:1510), gi|37147896 (SEQ ID NO:1511), gi|41351817 (SEQ ID NO:1512), gi|55824656 (SEQ ID NO:1513), gi|66269671 (SEQ ID NO:1514), gi|33638194 (SEQ ID NO:1515), and gi|21908034 (SEQ ID NO:1516).

The alignment in FIG. 101 provides the amino acid sequences of CeresClone:26867 (SEQ ID NO:1526) and Annot ID:1486918 (SEQ ID NO:1528).

The alignment in FIG. 112 provides the amino acid sequences of Ceres Clone 6397 (SEQ ID NO:1637), gi|57012876 (SEQ ID NO:1645), and gi|3342211 (SEQ ID NO:1651). Other homologs and/or orthologs of SEQ ID NO:1637 include Ceres CDNA ID no. 23401690 (SEQ ID NO:1638), Ceres CLONE ID no. 605218 (SEQ ID NO:1639), Public GI no. 57012759 (SEQ ID NO:1640), Ceres CLONE ID no. 282666 (SEQ ID NO:1641), Public GI no. 32401273 (SEQ ID NO:1642), Ceres CLONE ID no. 592713 (SEQ ID NO:1643), Public GI no. 3342211 (SEQ ID NO:1644), Ceres CLONE ID no. 555364 (SEQ ID NO:1646), Ceres CLONE ID no. 944101 (SEQ ID NO:1647), Ceres CLONE ID no. 569593 (SEQ ID NO:1648), Public GI no. 50927517 (SEQ ID NO:1649), Public GI no. 57012876 (SEQ ID NO:1650), and Ceres ANNOT ID no. 6064272 (SEQ ID NO:2290).

The alignment in FIG. 114 provides the amino acid sequences of CeresClone:681088 (SEQ ID NO:1661) and Annot ID:1471330 (SEQ ID NO:1663). Other homologs and/or orthologs of SEQ ID NO:1661 include Ceres ANNOT ID no. 1444437 (SEQ ID NO:1665), Ceres ANNOT ID no. 1444439 (SEQ ID NO:1667), Ceres ANNOT ID no. 1486891 (SEQ ID NO:1669), Ceres ANNOT ID no. 1479637 (SEQ ID NO:1671), and Ceres ANNOT ID no. 1446530 (SEQ ID NO:1673).

The alignment in FIG. 115 provides the amino acid sequences of CeresClone:691319 (SEQ ID NO:1675) and CeresClone:1475648 (SEQ ID NO:1676). Other homologs and/or orthologs of SEQ ID NO:1675 include Public GI no. 30725634 (SEQ ID NO:1677), Ceres ANNOT ID no. 1452324 (SEQ ID NO:1678), Ceres ANNOT ID no. 1443093 (SEQ ID NO:1679), and Ceres ANNOT ID no. 6014857 (SEQ ID NO:2188).

The alignment in FIG. 117 provides the amino acid sequences of CeresClone:92102 (SEQ ID NO:1692), CeresClone:965028, gi|45642990, gi|40060531, gi|38260618, and CeresClone:548557. Other homologs and/or orthologs of SEQ ID NO:1692 include Ceres ANNOT ID no. 1484557 (SEQ ID NO:1694) and Ceres ANNOT ID no. 1438401 (SEQ ID NO:1696).

The alignment in FIG. 122 provides the amino acid sequences of cDNA ID 23401690 (Ceres CLONE ID no. 603410; SEQ ID NO:1752), CeresClone:605218 (SEQ ID NO:1753), gi|57012759 (SEQ ID NO:1754), CeresClone:6397 (SEQ ID NO:1755), CeresClone:282666 (SEQ ID NO:1756), gi|32401273 (SEQ ID NO:1757), CeresClone:592713 (SEQ ID NO:1758), gi|3342211 (SEQ ID NO:1759), gi|57012876 (SEQ ID NO:1760), CeresClone:555364 (SEQ ID NO:1761), CeresClone:944101 (SEQ ID NO:1762), CeresClone:569593 (SEQ ID NO:1763), and gi|50927517 (SEQ ID NO:1764). Other homologs and/or orthologs of SEQ ID NO:1752 include Ceres CLONE ID no. 661590 (SEQ ID NO:1765) and Ceres ANNOT ID no. 6064272 (SEQ ID NO:2288).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:583 include Ceres CLONE ID no. 1897613 (SEQ ID NO:2149).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1062 include Ceres ANNOT ID no. 6015724 (SEQ ID NO:2190) and Ceres ANNOT ID no. 6111686 (SEQ ID NO:2346).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:1529-1533, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1053, SEQ ID NOs:1055-1056, SEQ ID NOs:1065-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NOs:1303-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NOs:1505-1516, SEQ ID NO:1528, SEQ ID NOs:1638-1651, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1676-1679, SEQ ID NO:1694, SEQ ID NO:1696, CeresClone:965028, gi|45642990, gi|40060531, gi|38260618, CeresClone:548557, SEQ ID NOs:1753-1765, SEQ ID NO:2149, SEQ ID NO:2162, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2234, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2308, SEQ ID NO:2344, or SEQ ID NO:2346.

A regulatory protein can contain a B3 DNA binding domain characteristic of a family of plant transcription factors with various roles in development. A B3 DNA binding domain is found in VP1/AB13 transcription factors. Some polypeptides, such as RAV1, also have an AP2 DNA binding domain. SEQ ID NO:835, SEQ ID NO:1285, and SEQ ID NO:1653 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 38961 (SEQ ID NO:834), Ceres CLONE ID no. 38311 (SEQ ID NO:1284), and Ceres CLONE ID no. 660003 (SEQ ID NO:1652), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a B3 DNA binding domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:835, SEQ ID NO:1285, or SEQ ID NO:1653. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:835, SEQ ID NO:1285, or SEQ ID NO:1653. For example, a regulatory protein can have an amino acid sequence with at least 50% sequence identity, e.g., 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:835, SEQ ID NO:1285, or SEQ ID NO:1653.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1285 and SEQ ID NO:1653 are provided in FIG. 77 and FIG. 113, respectively.

For example, the alignment in FIG. 77 provides the amino acid sequences of Ceres Clone 38311 (SEQ ID NO:1285), CeresClone:19561 (SEQ ID NO:1957), gi|33320073 (SEQ ID NO:1959), CeresClone:597624 (SEQ ID NO:1958), CeresClone:331400 (SEQ ID NO:1961), CeresClone:705041 (SEQ ID NO:1960), and gi|50932645 (SEQ ID NO:1962). Other homologs and/or orthologs of SEQ ID NO:1285 include Public GI no. 72140114 (SEQ ID NO:1287), Public GI no. 34895690 (SEQ ID NO:1290), and Ceres CLONE ID no. 1781615 (SEQ ID NO:1292).

The alignment in FIG. 113 provides the amino acid sequences of CeresClone:660003 (SEQ ID NO:1653), CeresClone:763852 (SEQ ID NO:1655), and Annot ID:1508184 (SEQ ID NO:1657). Other homologs and/or orthologs of SEQ ID NO:1653 include Public GI no. 26450255 (SEQ ID NO:1654), Ceres ANNOT ID no. 1528645 (SEQ ID NO:1659), and Ceres ANNOT ID no. 6038039 (SEQ ID NO:2258).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:1957-1962, SEQ ID NO:1287, SEQ ID NO:1290, SEQ ID NO:1292, SEQ ID NOs:1654-1655, SEQ ID NO:1657, SEQ ID NO:1659, or SEQ ID NO:2258.

In some cases, a regulatory protein can contain an AP2 domain described above and a B3 DNA binding domain described above. SEQ ID NO:1371 and SEQ ID NO:1844 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 597624 (SEQ ID NO:1370) and Ceres CLONE ID no. 19561 (SEQ ID NO:1843), respectively, each of which is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., an AP2 and a B3 DNA binding domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1371 or SEQ ID NO:1844. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1371 or SEQ ID NO:1844. For example, a regulatory protein can have an amino acid sequence with at least 50% sequence identity, e.g., 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1371 or SEQ ID NO:1844.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1371 are provided in FIG. 85.

For example, the alignment in FIG. 85 provides the amino acid sequences of cDNA ID 23402435 (Ceres CLONE ID no. 597624; SEQ ID NO:1371), gi|33320073 (SEQ ID NO:1288), and gi|15810645. Other homologs and/or orthologs of SEQ ID NO:1371 include Ceres ANNOT ID no. 1464039 (SEQ ID NO:1373) and Ceres CLONE ID no. 1781615 (SEQ ID NO:1375).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:1288, SEQ ID NO:1373, SEQ ID NO:1375, or gi|15810645.

A regulatory protein can contain a myb-like DNA binding domain characteristic of myb-like transcription factor polypeptides. The retroviral oncogene v-myb and its cellular counterpart c-myb encode nuclear DNA binding polypeptides. These polypeptides belong to the SANT domain family that specifically recognize the sequence YAAC(G/T)G. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA binding. Arabidopsis thaliana is estimated to contain more than 140 MYB or MYB-related genes. In contrast to animals, plants contain a MYB-protein subfamily that is characterized by the R2R3-type MYB domain. Classical MYB factors, which are related to c-MYB, seem to be involved in the control of the cell cycle in animals, plants and other higher eukaryotes. R2R3-type MYB genes control many aspects of plant secondary metabolism, as well as the identity and fate of plant cells. SEQ ID NO:518, SEQ ID NO:590, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NO:671, SEQ ID NO:703, SEQ ID NO:707, SEQ ID NO:814, SEQ ID NO:1383, SEQ ID NO:1395, SEQ ID NO:1518, SEQ ID NO:1540, SEQ ID NO:1552, SEQ ID NO:1570, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1842, and SEQ ID NO:1892 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 157740 (SEQ ID NO:517), Ceres CLONE ID no. 22671 (SEQ ID NO:589), Ceres CLONE ID no. 231109 (SEQ ID NO:598), Ceres CLONE ID no. 240112 (SEQ ID NO:600), Ceres CLONE ID no. 2942 (SEQ ID NO:670), Ceres CLONE ID no. 33139 (SEQ ID NO:702), Ceres CLONE ID no. 331755 (SEQ ID NO:706), Ceres CLONE ID no. 382267 (SEQ ID NO:813), Ceres CLONE ID no. 115924 (SEQ ID NO:1382), Ceres CLONE ID no. 120302 (SEQ ID NO:1394), Ceres CLONE ID no. 25795 (SEQ ID NO:1517), Ceres CLONE ID no. 325800 (SEQ ID NO:1539), Ceres CLONE ID no. 33333 (SEQ ID NO:1551), Ceres CLONE ID no. 34589 (SEQ ID NO:1569), Ceres CLONE ID no. 114074 (SEQ ID NO:1835), Ceres CLONE ID no. 143475 (SEQ ID NO:1837), Ceres CLONE ID no. 152630 (SEQ ID NO:1841), and Ceres LOCUS ID no. 1493072 (SEQ ID NO:1891), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a myb-like DNA binding domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:518, SEQ ID NO:590, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NO:671, SEQ ID NO:703, SEQ ID NO:707, SEQ ID NO:814, SEQ ID NO:1383, SEQ ID NO:1395, SEQ ID NO:1518, SEQ ID NO:1540, SEQ ID NO:1552, SEQ ID NO:1570, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1842, or SEQ ID NO:1892. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:518, SEQ ID NO:590, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NO:671, SEQ ID NO:703, SEQ ID NO:707, SEQ ID NO:814, SEQ ID NO:1383, SEQ ID NO:1395, SEQ ID NO:1518, SEQ ID NO:1540, SEQ ID NO:1552, SEQ ID NO:1570, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1842, or SEQ ID NO:1892. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:518, SEQ ID NO:590, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NO:671, SEQ ID NO:703, SEQ ID NO:707, SEQ ID NO:814, SEQ ID NO:1383, SEQ ID NO:1395, SEQ ID NO:1518, SEQ ID NO:1540, SEQ ID NO:1552, SEQ ID NO:1570, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1842, or SEQ ID NO:1892.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:590, SEQ ID NO:601, SEQ ID NO:671, SEQ ID NO:703, SEQ ID NO:707, SEQ ID NO:1383, SEQ ID NO:1395, SEQ ID NO:1518, SEQ ID NO:1540, SEQ ID NO:1552, SEQ ID NO:1570, and SEQ ID NO:1892 are provided in FIG. 30, FIG. 31, FIG. 36, FIG. 42, FIG. 43, FIG. 87, FIG. 88, FIG. 100, FIG. 102, FIG. 103, FIG. 105, and FIG. 129, respectively.

For example, the alignment in FIG. 30 provides the amino acid sequences of Ceres Clone 22671 (SEQ ID NO:590), CeresClone:1079601 (SEQ ID NO:591), 1483277 (SEQ ID NO:593), CeresClone:690625 (SEQ ID NO:594), 1467420 (SEQ ID NO:596), and gi|15042132 (SEQ ID NO:597). Other homologs and/or orthologs of SEQ ID NO:590 include Ceres ANNOT ID no. 6042920 (SEQ ID NO:2276).

The alignment in FIG. 31 provides the amino acid sequences of Ceres Clone 240112 (SEQ ID NO:601), CeresClone:1791988 (SEQ ID NO:603), and gi|50918981 (SEQ ID NO:604). Other homologs and/or orthologs of SEQ ID NO:601 include Ceres CLONE ID no. 1797459 (SEQ ID NO:2133) and Ceres ANNOT ID no. 6011964 (SEQ ID NO:2186).

The alignment in FIG. 36 provides the amino acid sequences of Ceres Clone 2942 (SEQ ID NO:671), CeresClone:1619846 (SEQ ID NO:672), gi|50925955 (SEQ ID NO:673), 1455934 (SEQ ID NO:675), and CeresClone:337432 (SEQ ID NO:676). Other homologs and/or orthologs of SEQ ID NO:671 include Ceres ANNOT ID no. 6064740 (SEQ ID NO:2292).

The alignment in FIG. 42 provides the amino acid sequences of Ceres Clone 33139 (SEQ ID NO:703), 1503188 (SEQ ID NO:705) and gi|21386951 (SEQ ID NO:2067).

The alignment in FIG. 43 provides the amino acid sequences of Ceres Clone 331755 (SEQ ID NO:707), CeresClone:1775942 (SEQ ID NO:709), gi|34913016 (SEQ ID NO:710), CeresClone:1723374 (SEQ ID NO:711), CeresClone:1847251 (SEQ ID NO:713), gi|38566494 (SEQ ID NO:716), CeresAnnot:1514100 (SEQ ID NO:718), CeresClone:638126 (SEQ ID NO:725), gi|7981380 (SEQ ID NO:726), gi|92894385 (SEQ ID NO:727), and gi|61652985 (SEQ ID NO:728). Other homologs and/or orthologs of SEQ ID NO:707 include Ceres CLONE ID no. 1916571 (SEQ ID NO:715), Ceres ANNOT ID no. 1450327 (SEQ ID NO:720), Ceres ANNOT ID no. 1460832 (SEQ ID NO:722), and Ceres CLONE ID no. 1927753 (SEQ ID NO:724).

The alignment in FIG. 87 provides the amino acid sequences of Ceres Clone 115924 (SEQ ID NO:1383), CeresClone:894637 (SEQ ID NO:1923), gi|50725048 (SEQ ID NO:1924), and CeresClone:477003 (SEQ ID NO:1922). Other homologs and/or orthologs of SEQ ID NO:1383 include Ceres ANNOT ID no. 1453127 (SEQ ID NO:1385), Ceres ANNOT ID no. 1506261 (SEQ ID NO:1387), Ceres ANNOT ID no. 1480332 (SEQ ID NO:1389), Ceres ANNOT ID no. 1454197 (SEQ ID NO:1391), Ceres ANNOT ID no. 6040047 (SEQ ID NO:2268), and Ceres ANNOT ID no. 6078685 (SEQ ID NO:2306).

The alignment in FIG. 88 provides the amino acid sequences of cDNA ID 23449314 (Ceres CLONE ID no. 120302; SEQ ID NO:1395), CeresClone:1459729 (SEQ ID NO:2032), gi|56749359 (SEQ ID NO:2019), gi|1167484 (SEQ ID NO:2027), gi|50726662 (SEQ ID NO:2028), gi|19053 (SEQ ID NO:2029), gi|47680445 (SEQ ID NO:2033), gi|39725415 (SEQ ID NO:2025), gi|31980095 (SEQ ID NO:2026), and gi|13346194 (SEQ ID NO:2023). Other homologs and/or orthologs of SEQ ID NO:1395 include Ceres ANNOT ID no. 1450548 (SEQ ID NO:1397), Ceres ANNOT ID no. 1460633 (SEQ ID NO:1399), Ceres ANNOT ID no. 1480232 (SEQ ID NO:1401), Ceres ANNOT ID no. 1478804 (SEQ ID NO:1403), Public GI no. 3941412 (SEQ ID NO:2020), Public GI no. 28628965 (SEQ ID NO:2021), Public GI no. 82308 (SEQ ID NO:2022), Public GI no. 42541167 (SEQ ID NO:2024), Public GI no. 19072766 (SEQ ID NO:2030), Public GI no. 50948275 (SEQ ID NO:2031), and Ceres CLONE ID no. 1963208 (SEQ ID NO:2159).

The alignment in FIG. 100 provides the amino acid sequences of Ceres Clone 25795 (SEQ ID NO:1518) and CeresClone:1104601. Other homologs and/or orthologs of SEQ ID NO:1518 include Ceres ANNOT ID no. 1471291 (SEQ ID NO:1520), Ceres ANNOT ID no. 1444391 (SEQ ID NO:1522), Ceres ANNOT ID no. 1488042 (SEQ ID NO:1524), and Ceres ANNOT ID no. 6042920 (SEQ ID NO:2278).

The alignment in FIG. 102 provides the amino acid sequences of cDNA ID 23792467 (Ceres CLONE ID no. 325800; SEQ ID NO:1540), gi|4519671, gi|32470645, CeresClone:677527, CeresClone:537360, and gi|4835766. Other homologs and/or orthologs of SEQ ID NO:1540 include Ceres ANNOT ID no. 1517851 (SEQ ID NO:1542), Ceres ANNOT ID no. 1464534 (SEQ ID NO:1544), Ceres ANNOT ID no. 1511678 (SEQ ID NO:1546), Ceres ANNOT ID no. 1458433 (SEQ ID NO:1548), and Ceres ANNOT ID no. 1529923 (SEQ ID NO:1550).

The alignment in FIG. 103 provides the amino acid sequences of cDNA ID 23377150 (Ceres CLONE ID no. 33333; SEQ ID NO:1552), CeresClone:543289 (SEQ ID NO:2036), gi|30575840 (SEQ ID NO:2034), and gi|22795039 (SEQ ID NO:2035). Other homologs and/or orthologs of SEQ ID NO:1552 include Ceres ANNOT ID no. 1501772 (SEQ ID NO:1554), Ceres ANNOT ID no. 1519164 (SEQ ID NO:1556), Ceres ANNOT ID no. 1480076 (SEQ ID NO:1558), Ceres ANNOT ID no. 1524008 (SEQ ID NO:1560), and Ceres ANNOT ID no. 1480159 (SEQ ID NO:1562).

The alignment in FIG. 105 provides the amino acid sequences of ME LINE ME01130 (Ceres CLONE ID no. 34589; SEQ ID NO:1570) and CeresClone:975220 (SEQ ID NO:1979). Other homologs and/or orthologs of SEQ ID NO:1570 include Ceres CLONE ID no. 539578 (SEQ ID NO:1571).

The alignment in FIG. 129 provides the amino acid sequences of Annot ID:1493072 (SEQ ID NO:1892), gi|39725413 (SEQ ID NO:1894) and gi|71041096 (SEQ ID NO:1895). Other homologs and/or orthologs of SEQ ID NO:1892 include Ceres ANNOT ID no. 1461478 (SEQ ID NO:1893).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1838 include Ceres ANNOT ID no. 1487827 (SEQ ID NO:2113), Ceres ANNOT ID no. 6040882 (SEQ ID NO:2270), and Ceres ANNOT ID no. 6108946 (SEQ ID NO:2372).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:599 include Ceres ANNOT ID no. 6018481 (SEQ ID NO:2218).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NOs:603-604, SEQ ID NOs:672-673, SEQ ID NOs:675-676, SEQ ID NO:705, SEQ ID NO:2067, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NOs:1922-1924, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:2019-2033, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, CeresClone:1104601, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, gi|4519671, gi|32470645, CeresClone:677527, CeresClone:537360, gi|4835766, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NOs:2034-2036, SEQ ID NO:1571, SEQ ID NO:1979, SEQ ID NOs:1893-1895, SEQ ID NO:2113, SEQ ID NO:2133, SEQ ID NO:2159, SEQ ID NO:2186, SEQ ID NO:2218, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2292, SEQ ID NO:2306, or SEQ ID NO:2342.

A regulatory protein can have an HLH (helix-loop-helix) DNA binding domain characteristic of basic-helix-loop-helix (bHLH) transcription factors. Basic-helix-loop-helix transcription factors belong to a family of transcriptional regulators present in eukaryotes. Many different functions have been identified for bHLH transcription factors in animals, including control of cell proliferation and development of specific cell lineages. In plants, bHLH transcription factors are thought to have various roles in plant cell and tissue development as well as plant metabolism. The mechanism whereby bHLH transcription factors control gene transcription often involves homo- or hetero-dimerization. Basic-helix-loop-helix transcription factors constitute one of the largest families of transcription factors in Arabidopsis thaliana. Comparisons with animal sequences suggest that the majority of plant bHLH genes have evolved from the ancestral group B class of bHLH genes. Twelve sub-families have been identified. Within each of these main groups, there are conserved amino acid sequence motifs outside the DNA binding domain. SEQ ID NO:409, SEQ ID NO:526, SEQ ID NO:566, SEQ ID NO:833, SEQ ID NO:1058, SEQ ID NO:1129, SEQ ID NO:1163, SEQ ID NO:1361, SEQ ID NO:1785, SEQ ID NO:1806, and SEQ ID NO:1872 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 118001 (SEQ ID NO:408), Ceres CLONE ID no. 16284 (SEQ ID NO:525), Ceres CLONE ID no. 21406 (SEQ ID NO:565), Ceres CLONE ID no. 388074 (SEQ ID NO:832), Ceres CLONE ID no. 558003 (SEQ ID NO:1057), Ceres CLONE ID no. 93825 (SEQ ID NO:1128), Ceres CLONE ID no. 98716 (SEQ ID NO:1162), Ceres CLONE ID no. 560948 (SEQ ID NO:1360), Ceres CLONE ID no. 8607 (SEQ ID NO:1784), Ceres CLONE ID no. 519 (SEQ ID NO:1805), and Ceres CLONE ID no. 35890 (SEQ ID NO:1871), respectively, each of which is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., an HLH DNA binding domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:409, SEQ ID NO:526, SEQ ID NO:566, SEQ ID NO:833, SEQ ID NO:1058, SEQ ID NO:1129, SEQ ID NO:1163, SEQ ID NO:1361, SEQ ID NO:1785, SEQ ID NO:1806, or SEQ ID NO:1872. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:409, SEQ ID NO:526, SEQ ID NO:566, SEQ ID NO:833, SEQ ID NO:1058, SEQ ID NO:1129, SEQ ID NO:1163, SEQ ID NO:1361, SEQ ID NO:1785, SEQ ID NO:1806, or SEQ ID NO:1872. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:409, SEQ ID NO:526, SEQ ID NO:566, SEQ ID NO:833, SEQ ID NO:1058, SEQ ID NO:1129, SEQ ID NO:1163, SEQ ID NO:1361, SEQ ID NO:1785, SEQ ID NO:1806, or SEQ ID NO:1872.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:526, SEQ ID NO:566, SEQ ID NO:1361, SEQ ID NO:1785, and SEQ ID NO:1806 are provided in FIG. 24, FIG. 28, FIG. 84, FIG. 125, and FIG. 126, respectively.

For example, the alignment in FIG. 24 provides the amino acid sequences of Ceres Clone 16284 (SEQ ID NO:526) and CeresClone:976709 (SEQ ID NO:527). Other homologs and/or orthologs of SEQ ID NO:526 include Ceres ANNOT ID no. 6106469 (SEQ ID NO:2338).

The alignment in FIG. 28 provides the amino acid sequences of Ceres Clone 21406 (SEQ ID NO:566), gi|24030386 (SEQ ID NO:567), gi|6850309 (SEQ ID NO:568), CeresAnnot:1498288 (SEQ ID NO:572), and CeresAnnot:1471938 (SEQ ID NO:574). Other homologs and/or orthologs of SEQ ID NO:566 include Ceres ANNOT ID no. 1525350 (SEQ ID NO:570), Public GI no. 34907702 (SEQ ID NO:575), Ceres CLONE ID no. 474693 (SEQ ID NO:576), Ceres ANNOT ID no. 1445304 (SEQ ID NO:578), Ceres CLONE ID no. 324760 (SEQ ID NO:579), Ceres CLONE ID no. 1940689 (SEQ ID NO:581), and Ceres CLONE ID no. 1806146 (SEQ ID NO:2063).

The alignment in FIG. 84 provides the amino acid sequences of CeresClone:560948 (SEQ ID NO:1361), Ceres Clone: 945972 (SEQ ID NO:1362), Ceres Clone: 503296 (SEQ ID NO:1367), and CeresClone:1759397 (SEQ ID NO:1369). Other homologs and/or orthologs of SEQ ID NO:1361 include Public GI no. 22331645 (SEQ ID NO:1363), Public GI no. 31431968 (SEQ ID NO:1364), Public GI no. 50912765 (SEQ ID NO:1365), and Ceres CLONE ID no. 486120 (SEQ ID NO:1366).

The alignment in FIG. 125 provides the amino acid sequences of cDNA ID 23557650 (Ceres CLONE ID no. 8607; SEQ ID NO:1785), CeresClone:1033993 (SEQ ID NO:1786), CeresClone:703180 (SEQ ID NO:1787), CeresClone:560681 (SEQ ID NO:1788), CeresClone:560948 (SEQ ID NO:1790), CeresClone:653656 (SEQ ID NO:1792), gi|50929085 (SEQ ID NO:1794), gi|50912765 (SEQ ID NO:1795), CeresClone:503296 (SEQ ID NO:1796), and CeresClone:486120 (SEQ ID NO:1797). Other homologs and/or orthologs of SEQ ID NO:1785 include Ceres CLONE ID no. 562428 (SEQ ID NO:1789), Ceres CLONE ID no. 630731 (SEQ ID NO:1791), Ceres CLONE ID no. 663844 (SEQ ID NO:1793), Ceres CLONE ID no. 237390 (SEQ ID NO:1798), Public GI no. 22331645 (SEQ ID NO:1799), Public GI no. 31431968 (SEQ ID NO:1800), Public GI no. 50912765 (SEQ ID NO:1801), Public GI no. 78708592 (SEQ ID NO:1802), Ceres CLONE ID no. 486120 (SEQ ID NO:1803), and Ceres CLONE ID no. 503296 (SEQ ID NO:1804).

The alignment in FIG. 126 provides the amino acid sequences of CeresClone:519 (SEQ ID NO:1806), CeresClone:951040 (SEQ ID NO:1811), CeresClone:703180 (SEQ ID NO:1814), and 1247092 (SEQ ID NO:1820). Other homologs and/or orthologs of SEQ ID NO:1806 include Public GI no. 90399109 (SEQ ID NO:1807), Public GI no. 21671920 (SEQ ID NO:1808), Ceres CLONE ID no. 609713 (SEQ ID NO:1809), Public GI no. 22331645 (SEQ ID NO:1810), Public GI no. 28416803 (SEQ ID NO:1812), Ceres CLONE ID no. 18200 (SEQ ID NO:1813), Ceres CLONE ID no. 560681 (SEQ ID NO:1815), Ceres CLONE ID no. 562428 (SEQ ID NO:1816), Ceres CLONE ID no. 560948 (SEQ ID NO:1817), Ceres CLONE ID no. 653656 (SEQ ID NO:1818), Ceres CLONE ID no. 663844 (SEQ ID NO:1819), and Ceres ANNOT ID no. 1468218 (SEQ ID NO:2105).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1163 include Ceres ANNOT ID no. 6016768 (SEQ ID NO:2208).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:409 include Ceres ANNOT ID no. 6039189 (SEQ ID NO:2260).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:527, SEQ ID NOs:567-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:2063, SEQ ID NOs:1362-1367, SEQ ID NO:1369, SEQ ID NOs:1786-1804, SEQ ID NOs:1807-1820, SEQ ID NO:2105, SEQ ID NO:2208, SEQ ID NO:2260, or SEQ ID NO:2338.

A regulatory protein can contain an SRF-TF domain characteristic of an SRF-type transcription factor (DNA binding and dimerization domain) polypeptide. Human serum response factor (SRF) is a ubiquitous nuclear polypeptide important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as the c-fos oncogene and muscle-specific actin genes. A core domain of about 90 amino acids is sufficient for the activities of DNA binding, dimerization, and interaction with accessory factors. Within the core is a DNA binding region, designated the MADS box, that is highly similar to many eukaryotic regulatory proteins, including the Agamous and Deficiens families of plant homeotic polypeptides. SEQ ID NO:461 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 1480 (SEQ ID NO:460), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an SRF-TF domain).

In some cases, a regulatory protein can contain an SRF-TF domain and a K-box region. Moreover, a K-box region is commonly found associated with SRF-type transcription factors. The K-box is predicted to have a coiled-coil structure and play a role in multimer formation. SEQ ID NO:760, SEQ ID NO:865, SEQ ID NO:980, and SEQ ID NO:1767 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 34635 (SEQ ID NO:759), Ceres CLONE ID no. 40334 (SEQ ID NO:864), Ceres CLONE ID no. 542773 (SEQ ID NO:979), and Ceres CLONE ID no. 32791 (SEQ ID NO:1766), respectively, each of which is predicted to encode a Pfam domain as indicated in the Sequence Listing (e.g., an SRF-type transcription factor polypeptide having a K-box region).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:461, SEQ ID NO:760, SEQ ID NO:865, SEQ ID NO:980, or SEQ ID NO:1767. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:461, SEQ ID NO:760, SEQ ID NO:865, SEQ ID NO:980, or SEQ ID NO:1767. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:461, SEQ ID NO:760, SEQ ID NO:865, SEQ ID NO:980, or SEQ ID NO:1767.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:461, SEQ ID NO:760, SEQ ID NO:865, SEQ ID NO:980, and SEQ ID NO:1767 are provided in FIG. 19, FIG. 47, FIG. 55, FIG. 61, and FIG. 123, respectively.

For example, the alignment in FIG. 19 provides the amino acid sequences of CeresClone:1480 (SEQ ID NO:461), CeresClone:1067639 (SEQ ID NO:462) and CeresClone:1068473 (SEQ ID NO:463). Other homologs and/or orthologs of SEQ ID NO:461 include Ceres ANNOT ID no. 6016483 (SEQ ID NO:2196).

The alignment in FIG. 47 provides the amino acid sequences of Ceres Clone 34635 (SEQ ID NO:760), gi|6707088 (SEQ ID NO:761), gi|48375197 (SEQ ID NO:762), gi|1561782 (SEQ ID NO:763), CeresClone:1921942 (SEQ ID NO:765), gi|1370276 (SEQ ID NO:766), gi|22665 (SEQ ID NO:767), gi|60858812 (SEQ ID NO:768), gi|82734191 (SEQ ID NO:769), gi|99109361 (SEQ ID NO:770), gi|42795301 (SEQ ID NO:771), gi|83999564 (SEQ ID NO:772), gi|42795285 (SEQ ID NO:773), gi|42795257 (SEQ ID NO:774), gi|16549070 (SEQ ID NO:775), gi|60100348 (SEQ ID NO:776), and gi|5825623 (SEQ ID NO:777).

The alignment in FIG. 55 provides the amino acid sequences of Ceres Clone 40334 (SEQ ID NO:865), gi|67043456 (SEQ ID NO:866), 1452158 (SEQ ID NO:868), gi|4105097 (SEQ ID NO:869), gi|56785938 (SEQ ID NO:870), CeresClone:1625939 (SEQ ID NO:871), gi|12666533 (SEQ ID NO:872), gi|60100344 (SEQ ID NO:873), gi|51832629 (SEQ ID NO:874), CeresClone:474230 (SEQ ID NO:875), gi|454265 (SEQ ID NO:876), gi|53988171 (SEQ ID NO:877), gi|48727608 (SEQ ID NO:878), gi|602902 (SEQ ID NO:879), gi|33338587 (SEQ ID NO:880), gi|4218173 (SEQ ID NO:881), gi|33309888 (SEQ ID NO:882), and gi|84578879 (SEQ ID NO:883). Other homologs and/or orthologs of SEQ ID NO:865 include Ceres ANNOT ID no. 6016483 (SEQ ID NO:2198) and Ceres ANNOT ID no. 6031322 (SEQ ID NO:2246).

The alignment in FIG. 61 provides the amino acid sequences of Ceres Clone 542773 (SEQ ID NO:980), CeresClone:1845589 (SEQ ID NO:982), gi|50924820 (SEQ ID NO:983), gi|34452085 (SEQ ID NO:984), gi|1816459 (SEQ ID NO:985), gi|15081463 (SEQ ID NO:986), gi|2959320 (SEQ ID NO:987), and gi|29611976 (SEQ ID NO:988). Other homologs and/or orthologs of SEQ ID NO:980 include Public GI no. 9964296 (SEQ ID NO:989), Public GI no. 30313677 (SEQ ID NO:990), Public GI no. 29028834 (SEQ ID NO:991), Public GI no. 63079855 (SEQ ID NO:992), Ceres ANNOT ID no. 6016517 (SEQ ID NO:2200), and Ceres ANNOT ID no. 6025104 (SEQ ID NO:2228).

The alignment in FIG. 123 provides the amino acid sequences of cDNA ID 23556617 (Ceres CLONE ID no. 32791; SEQ ID NO:1767), gi|1568513 (SEQ ID NO:1769), gi|20385590 (SEQ ID NO:1770), gi|27763670 (SEQ ID NO:1771), gi|60100358 (SEQ ID NO:1772), gi|48727598 (SEQ ID NO:1774), gi|21955182 (SEQ ID NO:1775), gi|3646326 (SEQ ID NO:1998), CeresClone:1044034 (SEQ ID NO:1999), gi|23194453 (SEQ ID NO:1997), gi|4103342 (SEQ ID NO:2000), gi|42794560 (SEQ ID NO:2003), gi|57157565 (SEQ ID NO:2002), and gi|29467048 (SEQ ID NO:2004). Other homologs and/or orthologs of SEQ ID NO:1767 include Public GI no. 30313671 (SEQ ID NO:1768), Public GI no. 42794566 (SEQ ID NO:1773), Ceres ANNOT ID no. 1540248 (SEQ ID NO:1777), Public GI no. 2997615 (SEQ ID NO:2001), and Public GI no. 1067169 (SEQ ID NO:2005).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:462-463, SEQ ID NOs:761-763, SEQ ID NOs:765-777, SEQ ID NO:866, SEQ ID NOs:868-883, SEQ ID NOs:982-992, SEQ ID NOs:1768-1775, SEQ ID NO:1777, SEQ ID NOs:1997-2005, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2228, or SEQ ID NO:2246.

A regulatory protein can have one or more domains characteristic of a basic-leucine zipper (bZIP) transcription factor polypeptide. For example, a regulatory protein can have a bZIP_(—)1 domain. The bZIP transcription factor polypeptides of eukaryotes contain a basic region mediating sequence-specific DNA binding and a leucine zipper region that is required for dimerization. In plants, bZIP transcription factors regulate processes including pathogen defense, light and stress signaling, seed maturation and flower development. The Arabidopsis genome sequence contains at least 70 distinct members of the bZIP family. SEQ ID NO:1840 and SEQ ID NO:1904 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 14432 (SEQ ID NO:1839) and Ceres CLONE ID no. 33016 (SEQ ID NO:1903), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a bZIP_(—)1 domain).

In some cases, a regulatory protein can contain a bZIP_(—)2 domain characteristic of a bZIP transcription factor polypeptide. SEQ ID NO:608 and SEQ ID NO:614 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 25211 (SEQ ID NO:607) and Ceres CLONE ID no. 2831 (SEQ ID NO:613), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a bZIP_(—)2 domain).

In some cases, a regulatory protein can have a bZIP_Maf domain and an MFMR domain, both of which are characteristic of basic region leucine zipper (bZIP) domain-containing transcription factor polypeptides. The Maf family of basic region leucine zipper (bZIP) domain-containing transcription factor polypeptides may be related to bZIP_(—)1. An MFMR region is found in the N-terminus of the bZIP_(—)1 transcription factor domain. The N-terminal half is rich in proline residues and has been termed the PRD (proline rich domain). The C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). SEQ ID NO:1735 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 834509 (SEQ ID NO:1734), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a bZIP_Maf domain and an MFMR domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1840, SEQ ID NO:1904, SEQ ID NO:608, SEQ ID NO:614, or SEQ ID NO:1735. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1840, SEQ ID NO:1904, SEQ ID NO:608, SEQ ID NO:614, or SEQ ID NO:1735. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1840, SEQ ID NO:1904, SEQ ID NO:608, SEQ ID NO:614, or SEQ ID NO:1735.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:614 and SEQ ID NO:1735 are provided in FIG. 32 and FIG. 121, respectively.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1904 include Ceres ANNOT ID no. 1451996 (SEQ ID NO:2097) and Ceres ANNOT ID no. 6006703 (SEQ ID NO:2166).

For example, the alignment in FIG. 32 provides the amino acid sequences of Ceres Clone 2831 (SEQ ID NO:614), CeresClone:1385680 (SEQ ID NO:617), CeresAnnot:1497776 (SEQ ID NO:619), gi|9650826 (SEQ ID NO:622), CeresClone:1728175 (SEQ ID NO:623), gi|2244744 (SEQ ID NO:624), CeresClone:676378 (SEQ ID NO:625), gi|77999786 (SEQ ID NO:626), gi|16580132 (SEQ ID NO:627), gi|3986151 (SEQ ID NO:629), gi|77556137 (SEQ ID NO:630), gi|72398495 (SEQ ID NO:631), gi|5901747 (SEQ ID NO:633), gi|40019253 (SEQ ID NO:634), and gi|62898531 (SEQ ID NO:635). Other homologs and/or orthologs of SEQ ID NO:614 include Public GI no. 15228754 (SEQ ID NO:615), Ceres CLONE ID no. 29982 (SEQ ID NO:616), Ceres ANNOT ID no. 1471578 (SEQ ID NO:621), Public GI no. 10241920 (SEQ ID NO:628), Public GI no. 72398497 (SEQ ID NO:632), and Ceres CLONE ID no. 869920 (SEQ ID NO:636).

The alignment in FIG. 121 provides the amino acid sequences of cDNA ID 23522373 5110H5 (Ceres ANNOT ID no. 834509; SEQ ID NO:1735), gi|3608135 (SEQ ID NO:1736), gi|3336903 (SEQ ID NO:1738), CeresClone:545441 (SEQ ID NO:1739), gi|5381313 (SEQ ID NO:1740), gi|3336906 (SEQ ID NO:1741), gi|13775109 (SEQ ID NO:1742), gi|435942 (SEQ ID NO:1743), and CeresClone:287677 (SEQ ID NO:1746). Other homologs and/or orthologs of SEQ ID NO:1735 include Ceres CLONE ID no. 1188156 (SEQ ID NO:1737), Ceres CLONE ID no. 523155 (SEQ ID NO:1744), Public GI no. 13775107 (SEQ ID NO:1745), Ceres ANNOT ID no. 1538994 (SEQ ID NO:1747), Ceres ANNOT ID no. 1447080 (SEQ ID NO:1749), and Ceres CLONE ID no. 1188156 (SEQ ID NO:1750).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:615-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:1736-1747, SEQ ID NOs:1749-1750, SEQ ID NO:2097, or SEQ ID NO:2166.

A regulatory protein can have a NAM domain characteristic of a No apical meristem (NAM) polypeptide. No apical meristem (NAM) polypeptides are plant development polypeptides. NAM is indicated as having a role in determining positions of meristems and primordia. The NAC domain (NAM for Petunia hybrida and ATAF1, ATAF2, and CUC2 for Arabidopsis) is an N-terminal module of about 160 amino acids, which is found in polypeptides of the NAC family of plant-specific transcriptional regulators (no apical meristem polypeptides). NAC proteins are involved in developmental processes, including formation of the shoot apical meristem, floral organs and lateral shoots, as well as in plant hormonal control and defense. The NAC domain is accompanied by diverse C-terminal transcriptional activation domains. The NAC domain has been shown to be a DNA-binding domain and a dimerization domain. SEQ ID NO:165, SEQ ID NO:413, SEQ ID NO:555, SEQ ID NO:1104, and SEQ ID NO:1830 set forth the amino acid sequences of DNA clones, identified herein as Ceres ANNOT ID no. 840236 (SEQ ID NO:164), Ceres CLONE ID no. 119460 (SEQ ID NO:412), Ceres CLONE ID no. 205648 (SEQ ID NO:554), Ceres CLONE ID no. 8334 (SEQ ID NO:1103), and Ceres CLONE ID no. 100085 (SEQ ID NO:1829), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a NAM domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:165, SEQ ID NO:413, SEQ ID NO:555, SEQ ID NO:1104, or SEQ ID NO:1830. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:165, SEQ ID NO:413, SEQ ID NO:555, SEQ ID NO:1104, or SEQ ID NO:1830. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:165, SEQ ID NO:413, SEQ ID NO:555, SEQ ID NO:1104, or SEQ ID NO:1830.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:165, SEQ ID NO:555, and SEQ ID NO:1104 are provided in FIG. 6, FIG. 27, and FIG. 67, respectively.

For example, the alignment in FIG. 6 provides the amino acid sequences of Annot ID 840236 (SEQ ID NO:165) and gi|21105736 (SEQ ID NO:168). Other homologs and/or orthologs of SEQ ID NO:165 include Public GI no. 8567777 (SEQ ID NO:166) and Public GI no. 42572353 (SEQ ID NO:167).

The alignment in FIG. 27 provides the amino acid sequences of Ceres Clone 205648 (SEQ ID NO:555), gi|102139801 (SEQ ID NO:556), gi|15148912 (SEQ ID NO:557), CeresClone:577178 (SEQ ID NO:558), CeresClone:644344 (SEQ ID NO:559), gi|52076897 (SEQ ID NO:560), CeresClone:1674566 (SEQ ID NO:561), CeresAnnot:1456842 (SEQ ID NO:563), and gi|34558777 (SEQ ID NO:564). Other homologs and/or orthologs of SEQ ID NO:555 include Ceres ANNOT ID no. 6090309 (SEQ ID NO:2322) and Ceres ANNOT ID no. 6099734 (SEQ ID NO:2334).

The alignment in FIG. 67 provides the amino acid sequences of Ceres Clone 8334 (SEQ ID NO:1104), gi|30984532 (SEQ ID NO:1105) and CeresClone:1923641 (SEQ ID NO:1125). Other homologs and/or orthologs of SEQ ID NO:1104 include Ceres CLONE ID no. 114858 (SEQ ID NO:1106), Ceres CLONE ID no. 1296788 (SEQ ID NO:1107), Ceres CLONE ID no. 1927853 (SEQ ID NO:1109), Ceres CLONE ID no. 673567 (SEQ ID NO:1110), Ceres CLONE ID no. 1306145 (SEQ ID NO:1111), Public GI no. 27529810 (SEQ ID NO:1112), Public GI no. 50924810 (SEQ ID NO:1113), Ceres CLONE ID no. 900490 (SEQ ID NO:1114), Ceres CLONE ID no. 1564140 (SEQ ID NO:1115), Ceres CLONE ID no. 1862399 (SEQ ID NO:1117), Ceres CLONE ID no. 835085 (SEQ ID NO:1118), Ceres CLONE ID no. 1562064 (SEQ ID NO:1119), Public GI no. 4218537 (SEQ ID NO:1120), Ceres CLONE ID no. 1821898 (SEQ ID NO:1122), Public GI no. 82400209 (SEQ ID NO:1123), Public GI no. 53749461 (SEQ ID NO:1126), Ceres CLONE ID no. 1603975 (SEQ ID NO:1127), and Ceres ANNOT ID no. 6112668 (SEQ ID NO:2348).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:166-168, SEQ ID NOs:556-561, SEQ ID NOs:563-564, SEQ ID NOs:1105-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:2322, SEQ ID NO:2334, or SEQ ID NO:2348.

A regulatory protein can contain an SBP domain. SBP (SQUAMOSA-PROMOTER BINDING PROTEIN) domains are found in plant polypeptides. The SBP plant polypeptide domain is a sequence specific DNA-binding domain. Polypeptides with this domain probably function as transcription factors involved in the control of early flower development. The domain contains 10 conserved cysteine and histidine residues that are likely to be zinc ligands. SEQ ID NO:1405 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 12071 (SEQ ID NO:1404), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an SBP domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1405. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1405. For example, a regulatory protein can have an amino acid sequence with at least 50% sequence identity, e.g., 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1405.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1405 are provided in FIG. 89.

For example, the alignment in FIG. 89 provides the amino acid sequences of Ceres Clone 12071 (SEQ ID NO:1405), gi|55419652 (SEQ ID NO:1406), gi|1183866 (SEQ ID NO:1407), CeresClone:538817 (SEQ ID NO:1408), gi|30577630 (SEQ ID NO:1409), and gi|62856979 (SEQ ID NO:2059). Other homologs and/or orthologs of SEQ ID NO:1405 include SEQ ID NO:1410, Ceres ANNOT ID no. 1466704 (SEQ ID NO:1412), Public GI no. 30577630 (SEQ ID NO:2058), and Ceres ANNOT ID no. 6032291 (SEQ ID NO:2252).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:1406-1410, SEQ ID NO:1412, SEQ ID NOs:2058-2059, or SEQ ID NO:2252.

A regulatory protein can have an mTERF domain. The human mitochondrial transcription termination factor (mTERF) polypeptide possesses three putative leucine zippers, one of which is bipartite. The mTERF polypeptide also contains two widely spaced basic domains. Both of the basic domains and the three leucine zipper motifs are necessary for DNA binding. The mTERF polypeptide binds DNA as a monomer. While evidence of intramolecular leucine zipper interactions exists, the leucine zippers are not implicated in dimerization, unlike other leucine zippers. SEQ ID NO:695 and SEQ ID NO:1728 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 325679 (SEQ ID NO:694) and Ceres Annot ID no. 574705 (SEQ ID NO:1727), respectively, each of which is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., an mTERF domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:695 or SEQ ID NO:1728. Alternatively, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:695 or SEQ ID NO:1728. For example, a regulatory protein can have an amino acid sequence with at least 60% sequence identity, e.g., 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:695 or SEQ ID NO:1728.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:695 and SEQ ID NO:1728 are provided in FIG. 40 and FIG. 120, respectively.

For example, the alignment in FIG. 40 provides the amino acid sequences of Ceres Clone 325679 (SEQ ID NO:695) and gi|50910213 (SEQ ID NO:696). Other homologs and/or orthologs of SEQ ID NO:695 include Ceres ANNOT ID no. 6023883 (SEQ ID NO:2226).

The alignment in FIG. 120 provides the amino acid sequences of cDNA ID 23653450 5109C6 (Ceres ANNOT ID no. 574705; SEQ ID NO:1728), gi|50938747 (SEQ ID NO:1729), CeresClone:458156 (SEQ ID NO:1730), and CeresClone:918824 (SEQ ID NO:1731). Other homologs and/or orthologs of SEQ ID NO:1728 include Ceres ANNOT ID no. 1441536 (SEQ ID NO:1733).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:696, SEQ ID NOs:1729-1731, SEQ ID NO:1733, or SEQ ID NO:2226.

A regulatory protein can have a TCP domain characteristic of a TCP family transcription factor polypeptide. Members of the TCP family contain conserved regions that are predicted to form a non-canonical basic-helix-loop-helix (bHLH) structure. In rice, this domain was shown to be involved in DNA binding and dimerization. In Arabidopsis, members of the TCP family were found to be expressed in rapidly growing floral primordia. It is likely that members of the TCP family affect cell division. SEQ ID NO:436 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 124496 (SEQ ID NO:435), that is predicted to encode a Pfam domain as indicated in the Sequence Listing (e.g., a TCP family transcription factor polypeptide).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:436. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:436. For example, a regulatory protein can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:436.

A regulatory protein can have a GRAS domain characteristic of a GRAS family transcription factor polypeptide. Polypeptides in the GRAS family are transcription factors that seem to be involved in development and other processes. For example, mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. The PATI protein is involved in phytochrome A signal transduction. GRAS polypeptides, such as GAI, RGA, and SCR, contain a conserved region of about 350 amino acids that can be divided into five motifs, found in the following order: the leucine heptad repeat I, the VHIID motif, the leucine heptad repeat II, the PFYRE motif, and the SAW motif. Plant specific GRAS polypeptides have parallels in their motif structure to the animal Signal Transducers and Activators of Transcription (STAT) family of polypeptides, which suggests parallels in their functions. SEQ ID NO:1294 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 109490 (SEQ ID NO:1293), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a GRAS domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1294. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1294. For example, a regulatory protein can have an amino acid sequence with at least 55% sequence identity, e.g., 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1294.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1294 are provided in FIG. 78.

For example, the alignment in FIG. 78 provides the amino acid sequences of cDNA ID 23365746 (Ceres CLONE ID no. 109490; SEQ ID NO:1294), CeresClone:475016 (SEQ ID NO:1976), CeresClone:1571937 (SEQ ID NO:1977), and gi|34907424 (SEQ ID NO:1978). Other homologs and/or orthologs of SEQ ID NO:1294 include Ceres ANNOT ID no. 1443194 (SEQ ID NO:1296), Ceres ANNOT ID no. 1505312 (SEQ ID NO:1298), Ceres CLONE ID no. 1810690 (SEQ ID NO:1300), and Ceres ANNOT ID no. 6016469 (SEQ ID NO:2194).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1976-1978, or SEQ ID NO:2194.

A regulatory protein can contain a Histone domain characteristic of a core histone H2A/H2B/H3/H4 polypeptide. The core histones, together with other DNA binding polypeptides, form a superfamily defined by a common fold and distant sequence similarities. Some polypeptides contain local homology domains related to the histone fold. SEQ ID NO:1249 and SEQ ID NO:1573 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 21604 (SEQ ID NO:1248) and Ceres CLONE ID no. 36272 (SEQ ID NO:1572), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a Histone domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1249 or SEQ ID NO:1573. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1249 or SEQ ID NO:1573. For example, a regulatory protein can have an amino acid sequence with at least 65% sequence identity, e.g., 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1249 or SEQ ID NO:1573.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1249 and SEQ ID NO:1573 are provided in FIG. 74 and FIG. 106, respectively.

For example, the alignment in FIG. 74 provides the amino acid sequences of cDNA ID 23383311 (Ceres CLONE ID no. 21604; SEQ ID NO:1249), CeresClone:824827 (SEQ ID NO:2018), CeresClone:245683 (SEQ ID NO:2015), CeresClone:1283552 (SEQ ID NO:2016), CeresClone:272426 (SEQ ID NO:2017), CeresClone:659723 (SEQ ID NO:2012), CeresClone:1585988 (SEQ ID NO:2014), and CeresClone:953644 (SEQ ID NO:2013). Other homologs and/or orthologs of SEQ ID NO:1249 include Ceres ANNOT ID no. 1473854 (SEQ ID NO:1251), Ceres ANNOT ID no. 1521997 (SEQ ID NO:1253), Ceres ANNOT ID no. 1468633 (SEQ ID NO:1255), and Ceres CLONE ID no. 1784110 (SEQ ID NO:1257).

The alignment in FIG. 106 provides the amino acid sequences of Ceres Clone 36272 (SEQ ID NO:1573), CeresClone:573215 (SEQ ID NO:1955), CeresClone:474481 (SEQ ID NO:1956), gi|1922964 (SEQ ID NO:1954), gi|6289057 (SEQ ID NO:1953), CeresClone:1911 (SEQ ID NO:1951), and gi|23505813 (SEQ ID NO:1952). Other homologs and/or orthologs of SEQ ID NO:1573 include Ceres ANNOT ID no. 1469342 (SEQ ID NO:1575), Ceres ANNOT ID no. 1513277 (SEQ ID NO:1577), and Ceres ANNOT ID no. 1470275 (SEQ ID NO:1579).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NOs:2012-2018, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, or SEQ ID NOs:1951-1956.

A regulatory protein can contain one or more domains characteristic of a transcription initiation factor polypeptide. For example, a regulatory protein can contain a TFIIF_beta domain characteristic of the beta subunit of transcription initiation factor IIF. Transcription initiation factor IIF (TFIIF) is a tetramer comprising two beta subunits associated with two alpha subunits. TFIIF interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. SEQ ID NO:119 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 549656 (SEQ ID NO:118), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a TFIIF_beta domain).

In some cases, a regulatory protein can have a TFIIA_gamma_N domain and a TFIIA_gamma_C domain characteristic of the N-terminal and the C-terminal domain, respectively, of the gamma subunit of TFIIA. TFIIA is a heterotrimer composed of alpha, beta, and gamma subunits. The N-terminal domain of the gamma subunit is a four helix bundle, while the C-terminal domain is a twelve stranded beta-barrel. The TFIIA heterotrimer is a general transcription initiation factor for genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region. This is the first step in the formation of a pre-initiation complex, which is followed by binding of the rest of the transcription machinery. SEQ ID NO:1323 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 225321 (SEQ ID NO:1322), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a TFIIA_gamma_N domain and a TFIIA_gamma_C domain).

In some cases, a regulatory protein can contain a TFIID_(—)30 kDa domain characteristic of the transcription initiation factor TFIID 23-30 kDa subunit. Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TATA binding protein subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. SEQ ID NO:1854 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 25793 (SEQ ID NO:1853), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a TFIID_(—)30 kDa domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:119, SEQ ID NO:1323, or SEQ ID NO:1854. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:119, SEQ ID NO:1323, or SEQ ID NO:1854. For example, a regulatory protein can have an amino acid sequence with at least 50% sequence identity, e.g., 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:119, SEQ ID NO:1323, or SEQ ID NO:1854.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:119, SEQ ID NO:1323, and SEQ ID NO:1854 are provided in FIG. 3, FIG. 81, and FIG. 128, respectively.

For example, the alignment in FIG. 3 provides the amino acid sequences of Annot ID 549656 (SEQ ID NO:119), CeresClone:463643 (SEQ ID NO:122), CeresAnnot:1442640 (SEQ ID NO:124), CeresClone:704938 (SEQ ID NO:127), CeresClone:281395 (SEQ ID NO:128), CeresClone:1784166 (SEQ ID NO:130), and gi|56785216 (SEQ ID NO:131). Other homologs and/or orthologs of SEQ ID NO:119 include Public GI no. 39545896 (SEQ ID NO:120), Ceres CLONE ID no. 24161 (SEQ ID NO:121), Ceres ANNOT ID no. 1452795 (SEQ ID NO:126), and Public GI no. 34909946 (SEQ ID NO:132).

The alignment in FIG. 81 provides the amino acid sequences of Ceres Clone 225321 (SEQ ID NO:1323), gi|1429228 (SEQ ID NO:1945), CeresClone:8364 (SEQ ID NO:1944), CeresClone:530235 (SEQ ID NO:1943), gi|57899877 (SEQ ID NO:1942), CeresClone:1541168 (SEQ ID NO:1939), gi|55585039 (SEQ ID NO:1941), and CeresClone:699465 (SEQ ID NO:1940). Other homologs and/or orthologs of SEQ ID NO:1323 include Ceres ANNOT ID no. 1504670 (SEQ ID NO:1325), Ceres ANNOT ID no. 1451585 (SEQ ID NO:1327), Ceres CLONE ID no. 1785734 (SEQ ID NO:1329), and Ceres CLONE ID no. 1886324 (SEQ ID NO:1331).

The alignment in FIG. 128 provides the amino acid sequences of CeresClone:25793 (SEQ ID NO:1854) and CeresClone:1881639 (SEQ ID NO:1856).

Other homologs and/or orthologs of SEQ ID NO:1854 include Ceres ANNOT ID no. 1477838 (SEQ ID NO:2109), Ceres CLONE ID no. 1877540 (SEQ ID NO:2139), and Ceres ANNOT ID no. 6073498 (SEQ ID NO:2304).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:120-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NOs:1939-1945, SEQ ID NO:1856, SEQ ID NO:2109, SEQ ID NO:2139, or SEQ ID NO:2304.

A regulatory protein can have a paired amphipathic helix (PAH) repeat. The PAH repeat may be distantly related to the helix-loop-helix motif, which mediates polypeptide-polypeptide interactions. Members of the PAH repeat family of polypeptides include the eukaryotic Sin 3 polypeptides, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin 3 polypeptides are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. SEQ ID NO:1852 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 250028 (SEQ ID NO:1851), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a PAH repeat).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1852. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1852. For example, a regulatory protein can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1852.

A regulatory protein can have one or more domains characteristic of a homeobox polypeptide. For example, a regulatory protein can contain a homeobox domain and a HALZ domain. The homeobox domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterized by two alpha-helices, which make intimate contacts with DNA and are joined by a short turn. Examples of homeodomain-containing polypeptides include transcriptional regulators encoded by hox genes that operate differential genetic programs along the anterior-posterior axis of animal bodies. The homeobox associated leucine zipper (HALZ) domain is a plant specific leucine zipper that is associated with a homeobox. SEQ ID NO:661 sets forth the amino acid sequence of a DNA clone, identified herein Ceres CLONE ID no. 2913 (SEQ ID NO:660), that is predicted to encode a polypeptide having a homeobox domain and a Pfam domain as indicated in the Sequence Listing (e.g., a HALZ domain).

In some cases, a regulatory protein can contain a homeobox domain described above, a KNOX1 domain, a KNOX2 domain, and an ELK domain. Knotted1-like homeobox (knox) genes encoding KNOX proteins have been isolated from various plants, including rice, barley, Arabidopsis, soybean, tomato, and tobacco. There are four putative functional domains that are conserved in plant KNOX proteins: the MEINOX domain, which can divided into two subdomains, KNOX1 and KNOX2; the GSE domain; the ELK domain; and the homeodomain. KNOX1 plays a role in suppressing target gene expression, and KNOX2 is thought to be necessary for homo-dimerization. The ELK domain has been postulated to be involved in nuclear localization, polypeptide-polypeptide interactions, and suppression of gene activation. SEQ ID NO:1473 and SEQ ID NO:1779 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 21240 (SEQ ID NO:1472) and Ceres CLONE ID no. 541719 (SEQ ID NO:1778), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a homeobox domain, a KNOX1 domain, a KNOX2 domain, and an ELK domain).

In some cases, a regulatory protein can contain a KNOX1 domain, a KNOX2 domain, and an ELK domain. SEQ ID NO:1832 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 106887 (SEQ ID NO:1831), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a KNOX1 domain, a KNOX2 domain, and an ELK domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:661, SEQ ID NO:1473, SEQ ID NO:1779, or SEQ ID NO:1832. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:661, SEQ ID NO:1473, SEQ ID NO:1779, or SEQ ID NO:1832. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:661, SEQ ID NO:1473, SEQ ID NO:1779, or SEQ ID NO:1832.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:661, SEQ ID NO:1779, and SEQ ID NO:1832 are provided in FIG. 35, FIG. 124, and FIG. 127, respectively.

For example, the alignment in FIG. 35 provides the amino acid sequences of Ceres Clone 2913 (SEQ ID NO:661), CeresClone:1384592 (SEQ ID NO:662), CeresClone:1121989 (SEQ ID NO:663), 1463575 (SEQ ID NO:665), gi|48209882 (SEQ ID NO:666), gi|48209945 (SEQ ID NO:667), gi|349379 (SEQ ID NO:668), and CeresClone:677386 (SEQ ID NO:669).

The alignment in FIG. 124 provides the amino acid sequences of CeresClone:541719 (SEQ ID NO:1779) and Annot ID:1535677 (SEQ ID NO:1783). Other homologs and/or orthologs of SEQ ID NO:1779 include Ceres ANNOT ID no. 1518918 (SEQ ID NO:1781), Ceres ANNOT ID no. 6011832 (SEQ ID NO:2184), Ceres ANNOT ID no. 6034341 (SEQ ID NO:2254), and Ceres ANNOT ID no. 6034346 (SEQ ID NO:2256).

The alignment in FIG. 127 provides the amino acid sequences of CeresClone:106887 (SEQ ID NO:1832) and 1796871 (SEQ ID NO:1834). Other homologs and/or orthologs of SEQ ID NO:1832 include Ceres ANNOT ID no. 1491629 (SEQ ID NO:2115) and Ceres ANNOT ID no. 6068623 (SEQ ID NO:2302).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1473 include Ceres CLONE ID no. 1826333 (SEQ ID NO:2135).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:662-663, SEQ ID NOs:665-669, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NO:1834, SEQ ID NO:2115, SEQ ID NO:2135, SEQ ID NO:2184, SEQ ID NO:2254, SEQ ID NO:2256, or SEQ ID NO:2302.

A regulatory protein can contain a PHD domain. The homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from, the C3HC4 type RING finger. Similar to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. The PHD finger may be involved in polypeptide-polypeptide interactions and assembly or activity of multicomponent complexes involved in transcriptional activation or repression. In addition, the interactions may be intra-molecular and important in maintaining the structural integrity of the polypeptide. SEQ ID NO:504 sets forth the amino acid sequence of a DNA clone, referred to herein as Ceres CLONE ID no. 156373 (SEQ ID NO:503), that is predicted to encode a Pfam domain as indicated in the Sequence Listing (e.g., a PHD domain-containing polypeptide).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:504. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:504. For example, a regulatory protein can have an amino acid sequence with at least 55% sequence identity, e.g., 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:504.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:504 are provided in FIG. 22.

For example, the alignment in FIG. 22 provides the amino acid sequences of Ceres Clone 156373 (SEQ ID NO:504), CeresClone:1393778 (SEQ ID NO:505), CeresAnnot:1518013 (SEQ ID NO:508), CeresClone:477995 (SEQ ID NO:511), gi|45387429 (SEQ ID NO:513), gi|34900462 (SEQ ID NO:514), and CeresClone:1826835 (SEQ ID NO:516). Other homologs and/or orthologs of SEQ ID NO:504 include Public GI no. 21536795 (SEQ ID NO:506), Ceres ANNOT ID no. 1511533 (SEQ ID NO:510), and Ceres CLONE ID no. 1170863 (SEQ ID NO:512).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:505-506, SEQ ID NO:508, SEQ ID NOs:510-514, or SEQ ID NO:516.

A regulatory protein can contain an HTH_(—)3 domain characteristic of members of a family of DNA binding helix-turn helix polypeptides that includes a bacterial plasmid copy control polypeptide, bacterial methylases, various bacteriophage transcription control polypeptides, and a vegetative specific polypeptide from Dictyostelium discoideum. SEQ ID NO:1874 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 474636 (SEQ ID NO:1873), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an HTH_(—)3 domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1874. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1874. For example, a regulatory protein can have an amino acid sequence with at least 40% sequence identity, e.g., 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1874.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1874 include Ceres CLONE ID no. 1775129 (SEQ ID NO:2125).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:2125.

A regulatory protein can contain a SAP domain and an Exo_endo_phos domain. The SAP motif, named after SAF-A/B, Acinus and PIAS, is a putative DNA binding domain found in diverse nuclear polypeptides involved in chromosomal organization. The Exo_endo_phos domain is characteristic of polypeptides belonging to the endonuclease/exonuclease/phosphatase family of polypeptides. This large family of polypeptides includes magnesium dependent endonucleases and phosphatases involved in intracellular signaling. For example, the endonuclease/exonuclease/phosphatase family includes AP endonuclease proteins, DNase I proteins, and Synaptojanin, an inositol-1,4,5-trisphosphate phosphatase. SEQ ID NO:149 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 554970 (SEQ ID NO:148), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a SAP domain and an Exo_endo_phos domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:149. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:149. For example, a regulatory protein can have an amino acid sequence with at least 50% sequence identity, e.g., 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:149.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:149 are provided in FIG. 5.

For example, the alignment in FIG. 5 provides the amino acid sequences of Annot ID 554970 (SEQ ID NO:149), CeresAnnot:1528227 (SEQ ID NO:151), gi|34908948 (SEQ ID NO:152), and CeresClone:1158508 (SEQ ID NO:154). Other homologs and/or orthologs of SEQ ID NO:149 include Public GI no. 55297696 (SEQ ID NO:153) and Ceres CLONE ID no. 1222684 (SEQ ID NO:155).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:151-155.

A regulatory protein can contain a PC4 domain characteristic of the transcriptional coactivator p15 (PC4) polypeptide. The p15 polypeptide has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal domain is disguised by the amino-terminal p15 domain. The activity of the p15 polypeptide is controlled by kinase polypeptides that target the regulatory domain. SEQ ID NO:172 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 1001761 (SEQ ID NO:171), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a PC4 domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:172. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:172. For example, a regulatory protein can have an amino acid sequence with at least 55% sequence identity, e.g., 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:172.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:172 are provided in FIG. 7.

For example, the alignment in FIG. 7 provides the amino acid sequences of CeresClone:1001761 (SEQ ID NO:172), CeresClone:955105 (SEQ ID NO:174) and CeresClone:1620054 (SEQ ID NO:175). Other homologs and/or orthologs of SEQ ID NO:172 include Public GI no. 28466805 (SEQ ID NO:173) and Ceres CLONE ID no. 1617036 (SEQ ID NO:176).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:173-176.

A regulatory protein can contain an RNA_POL_M_(—)15 KD domain characteristic of highly conserved small subunits of about 15 kDa found in RNA polymerase types I and II. These polypeptides contain a probable zinc finger in the N-terminus and a zinc ribbon in the C-terminus. SEQ ID NO:417 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 12256 (SEQ ID NO:416), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an RNA_POL_M_(—)15 KD domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:417. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:417. For example, a regulatory protein can have an amino acid sequence with at least 70% sequence identity, e.g., 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:417.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:417 are provided in FIG. 15.

For example, the alignment in FIG. 15 provides the amino acid sequences of CeresClone:12256 (SEQ ID NO:417), CeresClone:976830 (SEQ ID NO:418), gi|87240462 (SEQ ID NO:421), gi|77556133 (SEQ ID NO:422), CeresClone:305612 (SEQ ID NO:423), CeresClone:686862 (SEQ ID NO:424), and CeresClone:1113246 (SEQ ID NO:425). Other homologs and/or orthologs of SEQ ID NO:417 include Ceres CLONE ID no. 966126 (SEQ ID NO:419), Public GI no. 46359779 (SEQ ID NO:420), Ceres CLONE ID no. 676701 (SEQ ID NO:426), Ceres CLONE ID no. 727529 (SEQ ID NO:427), Ceres CLONE ID no. 218484 (SEQ ID NO:428), Ceres CLONE ID no. 342112 (SEQ ID NO:429), Public GI no. 108705695 (SEQ ID NO:430), Ceres CLONE ID no. 1890779 (SEQ ID NO:2147), Ceres ANNOT ID no. 6009977 (SEQ ID NO:2176), and Ceres ANNOT ID no. 6039826 (SEQ ID NO:2266).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:418-430, SEQ ID NO:2147, SEQ ID NO:2176, or SEQ ID NO:2266.

A regulatory protein can contain an AUX_IAA domain. The AUX/IAA family of genes are key regulators of auxin-modified gene expression. The plant hormone auxin (indole-3-acetic acid, IAA) regulates diverse cellular and developmental responses in plants. The AUX/IAA polypeptides act as repressors of auxin-induced gene expression, possibly by modulating the activity of DNA binding auxin response factors (ARFs). AUX/IAA and ARF are thought to interact through C-terminal polypeptide-polypeptide interaction domains found in both AUX/IAA and ARF. AUX/IAA polypeptides have also been reported to mediate light responses. Some members of the AUX/IAA family are longer, contain an N-terminal DNA binding domain, and may have an early function in the establishment of vascular and body patterns during embryonic and post-embryonic development in some plants. SEQ ID NO:606 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 2499 (SEQ ID NO:605), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an AUX_IAA domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:606. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:606. For example, a regulatory protein can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:606.

A regulatory protein can have a WD-40 repeat, also known as WD or beta-transducin repeats. WD-40 repeats are motifs that often terminate in a Trp-Asp (W-D) dipeptide. Polypeptides containing WD repeats have four to 16 repeating units, which are thought to form a circularized beta-propeller structure. WD-repeat polypeptides serve as an assembly platform for multiprotein complexes in which the repeating units serve as a rigid scaffold for polypeptide interactions. Examples of such complexes include G protein complexes, the beta subunits of which are beta-propellers; TAFII transcription factor complexes; and E3 ubiquitin ligase complexes. WD-repeat polypeptides form a large family of eukaryotic polypeptides implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. SEQ ID NO:1345 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 475689 (SEQ ID NO:1344), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a WD-40 repeat).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1345. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1345. For example, a regulatory protein can have an amino acid sequence with at least 60% sequence identity, e.g., 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1345.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1345 are provided in FIG. 83.

For example, the alignment in FIG. 83 provides the amino acid sequences of Ceres Clone 475689 (SEQ ID NO:1345), gi|50251896 (SEQ ID NO:1970), CeresClone:783774 (SEQ ID NO:1968), gi|37544703 (SEQ ID NO:1969), CeresClone:1151902 (SEQ ID NO:1964), gi|10636051 (SEQ ID NO:1965), gi|22324807 (SEQ ID NO:1963), gi|14270085 (SEQ ID NO:1971), gi|2290532 (SEQ ID NO:1967), and gi|6752886 (SEQ ID NO:1966). Other homologs and/or orthologs of SEQ ID NO:1345 include Ceres ANNOT ID no. 1472897 (SEQ ID NO:1347), Ceres ANNOT ID no. 1467673 (SEQ ID NO:1349), Ceres ANNOT ID no. 1445014 (SEQ ID NO:1351), Ceres ANNOT ID no. 1471808 (SEQ ID NO:1353), Ceres ANNOT ID no. 1454998 (SEQ ID NO:1355), Ceres ANNOT ID no. 1475212 (SEQ ID NO:1357), and Ceres CLONE ID no. 1821171 (SEQ ID NO:1359).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:1963-1971, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, or SEQ ID NO:1359.

A regulatory protein can contain an ankyrin repeat and a Chromo (CHRromatin Organization MOdifier) domain. The ankyrin repeat is one of the most common polypeptide-polypeptide interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. The repeat has been found in diverse polypeptides such as transcriptional initiators, cell-cycle regulators, cytoskeletal polypeptides, ion transporters, and signal transducers. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90 degree angle. The repeats stack together to form an L-shaped structure. The Chromo domain is a conserved region of about 60 amino acids that was originally identified in Drosophila modifiers of variegation. These polypeptides alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these polypeptides, Polycomb, the Chromo domain has been shown to be important for chromatin targeting. Polypeptides that contain a Chromo domain appear to fall into three classes. The first class includes polypeptides having an N-terminal Chromo domain followed by a region termed the Chromo shadow domain. Examples of such polypeptides include the Drosophila and human heterochromatin polypeptides Su(var)205 and HP1, respectively. The second class includes polypeptides with a single chromo domain, such as the Drosophila polypeptide Polycomb, mammalian modifier 3, human Mi-2 auto antigen, and several yeast and Caenorhabditis elegans hypothetical polypeptides. Paired tandem Chromo domains are found in polypeptides belonging to the third class, which includes mammalian DNA-binding/helicase polypeptides CHD-1 to CHD-4 and yeast polypeptide CHD1. SEQ ID NO:808 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 37980 (SEQ ID NO:807), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an ankyrin repeat and a Chromo domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:808. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:808. For example, a regulatory protein can have an amino acid sequence with at least 45% sequence identity, e.g., 45%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:808.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:808 are provided in FIG. 50.

For example, the alignment in FIG. 50 provides the amino acid sequences of Ceres Clone 37980 (SEQ ID NO:808), CeresClone:630887 (SEQ ID NO:809), 1460561 (SEQ ID NO:811), and gi|50919643 (SEQ ID NO:812). Other homologs and/or orthologs of SEQ ID NO:808 include Ceres ANNOT ID no. 6068499 (SEQ ID NO:2300).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:809, SEQ ID NOs:811-812, or SEQ ID NO:2300.

A regulatory protein can contain a methyl-CpG binding domain (MBD). Regulatory proteins with a methyl-CpG binding domain, in association with other polypeptides, have preferential binding affinity to methylated DNA, which results in changes in chromatin structure leading to transcriptional activation or transcriptional repression of affected genes. SEQ ID NO:934 and SEQ ID NO:1475 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 479015 (SEQ ID NO:933) and Ceres CLONE ID no. 21374 (SEQ ID NO:1474), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a methyl-CpG binding domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:934 or SEQ ID NO:1475. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:934 or SEQ ID NO:1475. For example, a regulatory protein can have an amino acid sequence with at least 50% sequence identity, e.g., 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:934 or SEQ ID NO:1475.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1475 are provided in FIG. 96.

For example, the alignment in FIG. 96 provides the amino acid sequences of CeresClone:21374 (SEQ ID NO:1475) and 1471763 (SEQ ID NO:1477). Other homologs and/or orthologs of SEQ ID NO:1475 include Ceres ANNOT ID no. 1482788 (SEQ ID NO:1479) and Ceres ANNOT ID no. 6031141 (SEQ ID NO:2244).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:1477, SEQ ID NO:1479, or SEQ ID NO:2244.

A regulatory protein can contain an HMG (high mobility group) box. HMG regulatory proteins can have one or more copies of an HMG-box motif or domain, and are involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these polypeptides regulate gene expression. SEQ ID NO:689, SEQ ID NO:1131, SEQ ID NO:1315, SEQ ID NO:1333, and SEQ ID NO:1444 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 31322 (SEQ ID NO:688), Ceres CLONE ID no. 963031 (SEQ ID NO:1130), Ceres CLONE ID no. 208429 (SEQ ID NO:1314), Ceres CLONE ID no. 333753 (SEQ ID NO:1332), and Ceres CLONE ID no. 16204 (SEQ ID NO:1443), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an HMG box).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:689, SEQ ID NO:1131, SEQ ID NO:1315, SEQ ID NO:1333, or SEQ ID NO:1444. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:689, SEQ ID NO:1131, SEQ ID NO:1315, SEQ ID NO:1333, or SEQ ID NO:1444. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:689, SEQ ID NO:1131, SEQ ID NO:1315, SEQ ID NO:1333, or SEQ ID NO:1444.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:689, SEQ ID NO:1131, SEQ ID NO:1315, SEQ ID NO:1333, and SEQ ID NO:1444 are provided in FIG. 39, FIG. 68, FIG. 80, FIG. 82, and FIG. 93, respectively.

For example, the alignment in FIG. 39 provides the amino acid sequences of Ceres Clone 31322 (SEQ ID NO:689), CeresClone:980901 (SEQ ID NO:690), CeresClone:1030653 (SEQ ID NO:691), CeresClone:956177 (SEQ ID NO:692), and CeresClone:1620744 (SEQ ID NO:693). Other homologs and/or orthologs of SEQ ID NO:689 include Ceres ANNOT ID no. 6023739 (SEQ ID NO:2224).

The alignment in FIG. 68 provides the amino acid sequences of Ceres Clone 963031 (SEQ ID NO:1131) and gi|21554154 (SEQ ID NO:1132). Other homologs and/or orthologs of SEQ ID NO:1131 include Ceres ANNOT ID no. 6030945 (SEQ ID NO:2242).

The alignment in FIG. 80 provides the amino acid sequences of cDNA ID 23740209 (Ceres CLONE ID no. 208429; SEQ ID NO:1315), CeresClone:471377 (SEQ ID NO:1985), CeresClone:207075 (SEQ ID NO:1982), gi|21554154 (SEQ ID NO:1983), gi|9759080 (SEQ ID NO:1984), CeresClone:617111 (SEQ ID NO:1981), and gi|50940237 (SEQ ID NO:1980). Other homologs and/or orthologs of SEQ ID NO:1315 include Ceres ANNOT ID no. 1457538 (SEQ ID NO:1317), Ceres ANNOT ID no. 1510743 (SEQ ID NO:1319), Ceres CLONE ID no. 1963116 (SEQ ID NO:1321), and Ceres ANNOT ID no. 6030945 (SEQ ID NO:2240).

The alignment in FIG. 82 provides the amino acid sequences of Ceres Clone 333753 (SEQ ID NO:1333), gi|50726318 (SEQ ID NO:1950), and gi|17017392 (SEQ ID NO:1949). Other homologs and/or orthologs of SEQ ID NO:1333 include Ceres ANNOT ID no. 1442401 (SEQ ID NO:1335), Ceres ANNOT ID no. 1506142 (SEQ ID NO:1337), Ceres CLONE ID no. 1802372 (SEQ ID NO:1339), Ceres CLONE ID no. 1891458 (SEQ ID NO:1341), Ceres CLONE ID no. 1762738 (SEQ ID NO:1343), and Ceres ANNOT ID no. 6031981 (SEQ ID NO:2248).

The alignment in FIG. 93 provides the amino acid sequences of cDNA ID 23358452 (Ceres CLONE ID no. 16204; SEQ ID NO:1444), CeresClone:873113 (SEQ ID NO:1449), CeresClone:956177 (SEQ ID NO:1450), CeresClone:721511 (SEQ ID NO:1451), CeresClone:641329 (SEQ ID NO:1452), CeresClone:782784 (SEQ ID NO:1453), gi|18645 (SEQ ID NO:1454), gi|1052956 (SEQ ID NO:1455), gi|436424 (SEQ ID NO:1456), gi|2894109 (SEQ ID NO:1457), CeresClone:686294 (SEQ ID NO:1458), gi|50726318 (SEQ ID NO:1459), gi|729737 (SEQ ID NO:1460), gi|729736 (SEQ ID NO:1461), CeresClone:1060767 (SEQ ID NO:1462), and gi|7446231 (SEQ ID NO:1463). Other homologs and/or orthologs of SEQ ID NO:1444 include Ceres CLONE ID no. 98140 (SEQ ID NO:1445), Ceres CLONE ID no. 480916 (SEQ ID NO:1147), and Ceres CLONE ID no. 1043468 (SEQ ID NO:1448).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:690-693, SEQ ID NO:1132, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NOs:1980-1985, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NOs:1949-1950, SEQ ID NO:1445, SEQ ID NOs:1447-1463, SEQ ID NO:2224, SEQ ID NO:2240, SEQ ID NO:2242, or SEQ ID NO:2248.

A regulatory protein can have an FHA domain. The FHA (forkhead-associated) domain is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but can also recognize phosphotyrosine with relatively high affinity. The FHA domain spans about 80-100 amino acid residues folded into an eleven-stranded beta sandwich, which sometimes contains small helical insertions between the loops connecting the strands. Genes encoding FHA-containing polypeptides have been identified in eubacterial and eukaryotic but not archaeal genomes. The FHA domain is present in a diverse range of polypeptides, such as kinases, phosphatases, kinesins, transcription factors, RNA binding proteins, and metabolic enzymes involved in many different cellular processes, such as DNA repair, signal transduction, vesicular transport, and protein degradation. SEQ ID NO:1864 and SEQ ID NO:2087 set forth the amino acid sequences of DNA clones, identified herein as Ceres Clone ID no. 280261 (SEQ ID NO:1863) and Ceres Clone ID no. 28026 (SEQ ID NO:2086), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an FHA domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1864 or SEQ ID NO:2087. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1864 or SEQ ID NO:2087. For example, a regulatory protein can have an amino acid sequence with at least 50% sequence identity, e.g., 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1864 or SEQ ID NO:2087.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1864 include Ceres CLONE ID no. 1776961 (SEQ ID NO:2127).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:2127.

A regulatory protein can have one or more RNA recognition motifs, also known as RRM, RBD, or RNP domains. For example, a regulatory protein can have an RRM_(—)1 RNA recognition motif. RNA recognition motifs are found in a variety of RNA binding polypeptides, including heterogeneous nuclear ribonucleoproteins (hnRNPs), polypeptides implicated in regulation of alternative splicing, and polypeptide components of small nuclear ribonucleoproteins (snRNPs). The RRM motif also appears in a few single stranded DNA binding polypeptides. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases. SEQ ID NO:178, SEQ ID NO:221, SEQ ID NO:361, SEQ ID NO:381, SEQ ID NO:432, SEQ ID NO:698, SEQ ID NO:1134, SEQ ID NO:1259, SEQ ID NO:1423, SEQ ID NO:1681, and SEQ ID NO:1860 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 1003205 (SEQ ID NO:177), Ceres CLONE ID no. 1011900 (SEQ ID NO:220), Ceres CLONE ID no. 112098 (SEQ ID NO:360), Ceres CLONE ID no. 115366 (SEQ ID NO:380), Ceres CLONE ID no. 123804 (SEQ ID NO:431), Ceres CLONE ID no. 32754 (SEQ ID NO:697), Ceres CLONE ID no. 97001 (SEQ ID NO:1133), Ceres CLONE ID no. 29637 (SEQ ID NO:1258), Ceres CLONE ID no. 14246 (SEQ ID NO:1422), Ceres CLONE ID no. 7559 (SEQ ID NO:1680), and Ceres CLONE ID no. 266712 (SEQ ID NO:1859), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a RRM_(—)1 domain).

In some cases, a regulatory protein containing an RRM_(—)1 domain can also contain a DnaJ domain associated with chaperone polypeptides involved in polypeptide folding. SEQ ID NO:779 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 362438 (SEQ ID NO:778), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an RRM_(—)1 domain and a DnaJ domain).

In some cases, a regulatory protein containing an RRM_(—)1 domain can also contain a galanin domain. Galanin is a highly conserved, 29 amino acid peptide that is processed from a larger precursor polypeptide. Galanin is believed to function as a neurotransmitter in mammals. Except in human, galanin is C-terminally amidated. SEQ ID NO:1866 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 280814 (SEQ ID NO:1865), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an RRM_(—)1 domain and a galanin domain).

In some cases, a regulatory protein containing an RRM_(—)1 domain can also contain a zf-CCHC domain described above. SEQ ID NO:170 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 844490 (SEQ ID NO:169), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., an RRM_(—)1 domain and a zf-CCHC domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:178, SEQ ID NO:221, SEQ ID NO:361, SEQ ID NO:381, SEQ ID NO:432, SEQ ID NO:698, SEQ ID NO:1134, SEQ ID NO:1259, SEQ ID NO:1423, SEQ ID NO:1681, SEQ ID NO:1860, SEQ ID NO:779, SEQ ID NO:1866, or SEQ ID NO:170. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:178, SEQ ID NO:221, SEQ ID NO:361, SEQ ID NO:381, SEQ ID NO:432, SEQ ID NO:698, SEQ ID NO:1134, SEQ ID NO:1259, SEQ ID NO:1423, SEQ ID NO:1681, SEQ ID NO:1860, SEQ ID NO:779, SEQ ID NO:1866, or SEQ ID NO:170. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:178, SEQ ID NO:221, SEQ ID NO:361, SEQ ID NO:381, SEQ ID NO:432, SEQ ID NO:698, SEQ ID NO:1134, SEQ ID NO:1259, SEQ ID NO:1423, SEQ ID NO:1681, SEQ ID NO:1860, SEQ ID NO:779, SEQ ID NO:1866, or SEQ ID NO:170.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:178, SEQ ID NO:221, SEQ ID NO:361, SEQ ID NO:381, SEQ ID NO:432, SEQ ID NO:698, SEQ ID NO:1259, SEQ ID NO:1423, and SEQ ID NO:1681 are provided in FIG. 8, FIG. 9, FIG. 12, FIG. 14, FIG. 16, FIG. 41, FIG. 75, FIG. 91, and FIG. 116, respectively.

For example, the alignment in FIG. 8 provides the amino acid sequences of CeresClone:1003205 (SEQ ID NO:178), CeresClone:1120014 (SEQ ID NO:179), CeresClone:1066826 (SEQ ID NO:180), CeresClone:1465358 (SEQ ID NO:185), gi|18347 (SEQ ID NO:186), CeresClone:1012773 (SEQ ID NO:190), gi|1346180 (SEQ ID NO:192), gi|469070 (SEQ ID NO:194), CeresAnnot:1450324 (SEQ ID NO:196), gi|2624326 (SEQ ID NO:199), CeresClone:815584 (SEQ ID NO:201), and CeresClone:1898837 (SEQ ID NO:217). Other homologs and/or orthologs of SEQ ID NO:178 include Ceres CLONE ID no. 1110162 (SEQ ID NO:181), Public GI no. 17819 (SEQ ID NO:182), Ceres CLONE ID no. 1416673 (SEQ ID NO:183), Ceres CLONE ID no. 1076411 (SEQ ID NO:184), Ceres CLONE ID no. 873740 (SEQ ID NO:187), Ceres CLONE ID no. 1075035 (SEQ ID NO:188), Ceres CLONE ID no. 1083222 (SEQ ID NO:189), Ceres CLONE ID no. 1385361 (SEQ ID NO:191), Ceres CLONE ID no. 1011900 (SEQ ID NO:193), Ceres ANNOT ID no. 1460836 (SEQ ID NO:198), Public GI no. 108863012 (SEQ ID NO:200), Ceres CLONE ID no. 751438 (SEQ ID NO:202), Ceres CLONE ID no. 924811 (SEQ ID NO:203), Ceres CLONE ID no. 741793 (SEQ ID NO:204), Ceres CLONE ID no. 754335 (SEQ ID NO:205), Ceres CLONE ID no. 761865 (SEQ ID NO:206), Ceres CLONE ID no. 785819 (SEQ ID NO:207), Ceres CLONE ID no. 758560 (SEQ ID NO:208), Ceres CLONE ID no. 1467901 (SEQ ID NO:209), Ceres CLONE ID no. 702924 (SEQ ID NO:210), Ceres CLONE ID no. 737259 (SEQ ID NO:211), Ceres CLONE ID no. 867872 (SEQ ID NO:212), Ceres CLONE ID no. 617713 (SEQ ID NO:213), Ceres CLONE ID no. 756168 (SEQ ID NO:214), Ceres CLONE ID no. 731572 (SEQ ID NO:215), and Ceres CLONE ID no. 1834630 (SEQ ID NO:219).

The alignment in FIG. 9 provides the amino acid sequences of CeresClone:1011900 (SEQ ID NO:221), CeresClone:1083222 (SEQ ID NO:222), CeresClone:1075035 (SEQ ID NO:223), CeresClone:1444599 (SEQ ID NO:225), gi|1346181 (SEQ ID NO:227), CeresClone:1053672 (SEQ ID NO:231), gi|469070 (SEQ ID NO:232), gi|2226370 (SEQ ID NO:234), gi|2267569 (SEQ ID NO:235), gi|18347 (SEQ ID NO:244), gi|34851124 (SEQ ID NO:246), gi|7024451 (SEQ ID NO:247), gi|6273331 (SEQ ID NO:248), gi|20152613 (SEQ ID NO:249), gi|92874469 (SEQ ID NO:250), CeresAnnot:1450324 (SEQ ID NO:253), gi|1229138 (SEQ ID NO:256), CeresClone:1834392 (SEQ ID NO:258), gi|108863012 (SEQ ID NO:263), gi|6911144 (SEQ ID NO:270), CeresClone:1773631 (SEQ ID NO:275), gi|1934994 (SEQ ID NO:290), gi|2674201 (SEQ ID NO:296), gi|799015 (SEQ ID NO:297), gi|4704605 (SEQ ID NO:311), gi|10799202 (SEQ ID NO:313), gi|90265701 (SEQ ID NO:316), gi|90704785 (SEQ ID NO:319), gi|21625 (SEQ ID NO:326), and gi|21388658 (SEQ ID NO:335). Other homologs and/or orthologs of SEQ ID NO:221 include Ceres CLONE ID no. 873740 (SEQ ID NO:224), Ceres CLONE ID no. 965777 (SEQ ID NO:226), Ceres CLONE ID no. 973585 (SEQ ID NO:228), Ceres CLONE ID no. 1092319 (SEQ ID NO:229), Ceres CLONE ID no. 945779 (SEQ ID NO:230), Public GI no. 30692254 (SEQ ID NO:233), Public GI no. 469071 (SEQ ID NO:236), Public GI no. 469072 (SEQ ID NO:237), Ceres CLONE ID no. 1120014 (SEQ ID NO:238), Ceres CLONE ID no. 102331 (SEQ ID NO:239), Public GI no. 16305 (SEQ ID NO:240), Ceres CLONE ID no. 14187 (SEQ ID NO:241), Ceres CLONE ID no. 13439 (SEQ ID NO:242), Ceres CLONE ID no. 32548 (SEQ ID NO:243), Ceres CLONE ID no. 1003147 (SEQ ID NO:245), Ceres CLONE ID no. 1110162 (SEQ ID NO:251), Ceres ANNOT ID no. 1460836 (SEQ ID NO:255), Ceres CLONE ID no. 1846800 (SEQ ID NO:260), Ceres CLONE ID no. 1884333 (SEQ ID NO:262), Public GI no. 108710320 (SEQ ID NO:264), Public GI no. 108710321 (SEQ ID NO:265), Ceres CLONE ID no. 1916226 (SEQ ID NO:267), Ceres CLONE ID no. 1898837 (SEQ ID NO:269), Ceres CLONE ID no. 1944006 (SEQ ID NO:272), Public GI no. 6911146 (SEQ ID NO:273), Public GI no. 6911142 (SEQ ID NO:276), Public GI no. 77557139 (SEQ ID NO:277), Ceres CLONE ID no. 1954236 (SEQ ID NO:279), Public GI no. 18103931 (SEQ ID NO:280), Ceres CLONE ID no. 1848150 (SEQ ID NO:282), Ceres CLONE ID no. 1759817 (SEQ ID NO:284), Ceres CLONE ID no. 1792432 (SEQ ID NO:286), Public GI no. 18076086 (SEQ ID NO:287), Ceres CLONE ID no. 1967547 (SEQ ID NO:289), Ceres CLONE ID no. 1772920 (SEQ ID NO:292), Ceres CLONE ID no. 1962722 (SEQ ID NO:294), Public GI no. 2331131 (SEQ ID NO:295), Public GI no. 2331133 (SEQ ID NO:298), Ceres CLONE ID no. 1959885 (SEQ ID NO:300), Ceres CLONE ID no. 1834630 (SEQ ID NO:302), Ceres CLONE ID no. 1810211 (SEQ ID NO:304), Ceres CLONE ID no. 1905168 (SEQ ID NO:306), Ceres CLONE ID no. 1888162 (SEQ ID NO:308), Public GI no. 2645699 (SEQ ID NO:309), Public GI no. 108710322 (SEQ ID NO:310), Public GI no. 2624326 (SEQ ID NO:312), Ceres CLONE ID no. 1966343 (SEQ ID NO:315), Ceres CLONE ID no. 1767411 (SEQ ID NO:318), Ceres CLONE ID no. 1789498 (SEQ ID NO:321), Ceres CLONE ID no. 1768120 (SEQ ID NO:323), Ceres CLONE ID no. 1762613 (SEQ ID NO:325), Ceres CLONE ID no. 1767462 (SEQ ID NO:328), Ceres CLONE ID no. 1721386 (SEQ ID NO:330), Ceres CLONE ID no. 1821019 (SEQ ID NO:332), and Ceres CLONE ID no. 1959598 (SEQ ID NO:334).

The alignment in FIG. 12 provides the amino acid sequences of CeresClone:112098 (SEQ ID NO:361), CeresClone:1376604 (SEQ ID NO:367) and CeresClone:463184 (SEQ ID NO:368). Other homologs and/or orthologs of SEQ ID NO:361 include Public GI no. 21593120 (SEQ ID NO:362), Ceres CLONE ID no. 38780 (SEQ ID NO:363), Ceres CLONE ID no. 36337 (SEQ ID NO:364), Public GI no. 30697598 (SEQ ID NO:365), and Public GI no. 30697595 (SEQ ID NO:366).

The alignment in FIG. 14 provides the amino acid sequences of CeresClone:115366 (SEQ ID NO:381), CeresClone:1376400 (SEQ ID NO:382), CeresClone:1834350 (SEQ ID NO:387), CeresClone:518274 (SEQ ID NO:389), gi|82400162 (SEQ ID NO:392), CeresAnnot:1446310 (SEQ ID NO:394), gi|6996560 (SEQ ID NO:395), gi|77551976 (SEQ ID NO:396), gi|92891800 (SEQ ID NO:398), CeresClone:1790416 (SEQ ID NO:400), and CeresClone:703017 (SEQ ID NO:403). Other homologs and/or orthologs of SEQ ID NO:381 include Public GI no. 13194792 (SEQ ID NO:383), Public GI no. 30695647 (SEQ ID NO:384), Ceres CLONE ID no. 148506 (SEQ ID NO:385), Public GI no. 21553830 (SEQ ID NO:388), Ceres CLONE ID no. 1836485 (SEQ ID NO:391), Public GI no. 108864589 (SEQ ID NO:397), Ceres CLONE ID no. 1754564 (SEQ ID NO:402), and Ceres ANNOT ID no. 6091796 (SEQ ID NO:2324).

The alignment in FIG. 16 provides the amino acid sequences of CeresClone:123804 (SEQ ID NO:432) and CeresClone:670908 (SEQ ID NO:433). Other homologs and/or orthologs of SEQ ID NO:432 include Ceres CLONE ID no. 614500 (SEQ ID NO:434).

The alignment in FIG. 41 provides the amino acid sequences of Ceres Clone 32754 (SEQ ID NO:698), CeresClone:1855403 (SEQ ID NO:700) and CeresClone:572426 (SEQ ID NO:701). Other homologs and/or orthologs of SEQ ID NO:698 include Ceres ANNOT ID no. 6023650 (SEQ ID NO:2222).

The alignment in FIG. 75 provides the amino acid sequences of Ceres Clone 29637 (SEQ ID NO:1259) and gi|34896798 (SEQ ID NO:1946). Other homologs and/or orthologs of SEQ ID NO:1259 include Ceres ANNOT ID no. 1458617 (SEQ ID NO:1261), Ceres ANNOT ID no. 1464333 (SEQ ID NO:1263), and Ceres CLONE ID no. 1787181 (SEQ ID NO:1265).

The alignment in FIG. 91 provides the amino acid sequences of Ceres Clone 14246 (SEQ ID NO:1423), gi|3550485 (SEQ ID NO:1424), CeresClone:1537388 (SEQ ID NO:1425), CeresClone:511197 (SEQ ID NO:1426), gi|50934311 (SEQ ID NO:1929), gi|311952 (SEQ ID NO:1926), and gi|20005 (SEQ ID NO:1927). Other homologs and/or orthologs of SEQ ID NO:1423 include SEQ ID NO:1427, gi|311952 (SEQ ID NO:1428), gi|115470657 (SEQ ID NO:1429), Ceres ANNOT ID no. 1454534 (SEQ ID NO:1431), Ceres ANNOT ID no. 1507701 (SEQ ID NO:1433), Ceres CLONE ID no. 511197 (SEQ ID NO:1925), Ceres CLONE ID no. 1537388 (SEQ ID NO:1928), Ceres CLONE ID no. 1537388 (SEQ ID NO:1930), and Ceres ANNOT ID no. 6011590 (SEQ ID NO:2182).

The alignment in FIG. 116 provides the amino acid sequences of cDNA ID 23380615 (Ceres CLONE ID no. 7559; SEQ ID NO:1681), CeresClone:844350 (SEQ ID NO:1685), gi|52140009 (SEQ ID NO:1686), CeresClone:298172 (SEQ ID NO:1687), gi|52140013 (SEQ ID NO:1688), CeresClone:541062 (SEQ ID NO:1689), gi|52140015 (SEQ ID NO:1690), and gi|52140010 (SEQ ID NO:2006). Other homologs and/or orthologs of SEQ ID NO:1681 include Ceres ANNOT ID no. 1469241 (SEQ ID NO:1683), SEQ ID NO:1684, Ceres CLONE ID no. 844350 (SEQ ID NO:1685), Ceres CLONE ID no. 1950861 (SEQ ID NO:2153), and Ceres ANNOT ID no. 6029526 (SEQ ID NO:2236).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:779 include Ceres ANNOT ID no. 1451365 (SEQ ID NO:2095).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1866 include Ceres ANNOT ID no. 1485544 (SEQ ID NO:2111), Ceres CLONE ID no. 1826678 (SEQ ID NO:2137), and Ceres ANNOT ID no. 6026295 (SEQ ID NO:2232).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:179-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:222-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NOs:362-368, SEQ ID NOs:382-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NOs:433-434, SEQ ID NOs:700-701, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1946, SEQ ID NOs:1424-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1925-1930, SEQ ID NO:1683-1690, SEQ ID NO:2006, SEQ ID NO:2095, SEQ ID NO:2111, SEQ ID NO:2137, SEQ ID NO:2153, SEQ ID NO:2182, SEQ ID NO:2222, SEQ ID NO:2232, SEQ ID NO:2236, or SEQ ID NO:2324.

A regulatory protein can have a G-patch domain. The D111/G-patch domain is a short conserved region of about 40 amino acids that occurs in a number of putative RNA-binding polypeptides, including tumor suppressor and DNA-damage-repair polypeptides. The G-patch domain may, therefore, have an RNA binding function. There are seven highly conserved glycine residues in the G-patch domain. SEQ ID NO:1564 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 333416 (SEQ ID NO:1563), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a G-patch domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1564. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1564. For example, a regulatory protein can have an amino acid sequence with at least 60% sequence identity, e.g., 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1564.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1564 are provided in FIG. 104.

For example, the alignment in FIG. 104 provides the amino acid sequences of Ceres Clone 333416 (SEQ ID NO:1564), CeresClone:108509 (SEQ ID NO:1947) and CeresClone:764678 (SEQ ID NO:1948). Other homologs and/or orthologs of SEQ ID NO:1564 include Ceres ANNOT ID no. 1469082 (SEQ ID NO:1566) and Ceres ANNOT ID no. 1522474 (SEQ ID NO:1568).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:1566, SEQ ID NO:1568, or SEQ ID NOs:1947-1948.

A regulatory protein can contain one or more domains characteristic of a helicase polypeptide. For example, a regulatory protein can contain a DEAD domain characteristic of DEAD/DEAH box helicase polypeptides. Members of the DEAD/DEAH box helicase polypeptide family include the DEAD and DEAH box helicases, which are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay, and organellar gene expression. SEQ ID NO:1581 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 389585 (SEQ ID NO:1580), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a DEAD domain).

In some cases, a regulatory protein can contain a DEAD domain and a Helicase_C domain. The Helicase_C, or helicase conserved C-terminal, domain is found in a wide variety of helicases and related polypeptides. The Helicase_C domain may be an integral part of the helicase rather than an autonomously folding unit. SEQ ID NO:938 and SEQ ID NO:1610 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 534281 (SEQ ID NO:937) and Ceres CLONE ID no. 42530 (SEQ ID NO:1609), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a DEAD domain and a Helicase_C domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1581, SEQ ID NO:938, or SEQ ID NO:1610. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1581, SEQ ID NO:938, or SEQ ID NO:1610. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1581, SEQ ID NO:938, or SEQ ID NO:1610.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:938 and SEQ ID NO:1610 are provided in FIG. 59 and FIG. 109, respectively.

For example, the alignment in FIG. 59 provides the amino acid sequences of Ceres Clone 534281 (SEQ ID NO:938), gi|92877732 (SEQ ID NO:939), CeresAnnot:1471100 (SEQ ID NO:943), gi|21280839 (SEQ ID NO:946), gi|50911116 (SEQ ID NO:947), CeresClone:1580901 (SEQ ID NO:950), CeresClone:703763 (SEQ ID NO:954), and CeresClone:1795581 (SEQ ID NO:959). Other homologs and/or orthologs of SEQ ID NO:938 include Public GI no. 92877736 (SEQ ID NO:940), Public GI no. 92877733 (SEQ ID NO:941), Ceres ANNOT ID no. 1497192 (SEQ ID NO:945), Public GI no. 3775993 (SEQ ID NO:948), Public GI no. 50926692 (SEQ ID NO:949), Ceres CLONE ID no. 236189 (SEQ ID NO:951), Public GI no. 50911118 (SEQ ID NO:952), Public GI no. 7267405 (SEQ ID NO:953), Ceres CLONE ID no. 777111 (SEQ ID NO:955), Public GI no. 37535822 (SEQ ID NO:956), Public GI no. 78708877 (SEQ ID NO:957), Ceres CLONE ID no. 290675 (SEQ ID NO:960), Public GI no. 62733592 (SEQ ID NO:961), Public GI no. 23197660 (SEQ ID NO:962), Ceres ANNOT ID no. 6094284 (SEQ ID NO:2330), and Ceres ANNOT ID no. 6094287 (SEQ ID NO:2332).

The alignment in FIG. 109 provides the amino acid sequences of Ceres CLONE ID no. 42530 (SEQ ID NO:1610), CeresClone:30700 (SEQ ID NO:2068), gi|19698881 (SEQ ID NO:2070), gi|25809054 (SEQ ID NO:2083), gi|2119932 (SEQ ID NO:2076), gi|19697 (SEQ ID NO:2071), gi|475216 (SEQ ID NO:2073), and gi|2119933 (SEQ ID NO:2080). Other homologs and/or orthologs of SEQ ID NO:1610 include Public GI no. 23397033 (SEQ ID NO:2069), Public GI no. 21555870 (SEQ ID NO:2072), Public GI no. 2119938 (SEQ ID NO:2074), Public GI no. 2119934 (SEQ ID NO:2075), Public GI no. 485949 (SEQ ID NO:2077), Public GI no. 485945 (SEQ ID NO:2078), Public GI no. 485943 (SEQ ID NO:2079), Public GI no. 485951 (SEQ ID NO:2081), Public GI no. 485987 (SEQ ID NO:2082), and Ceres CLONE ID no. 1792937 (SEQ ID NO:2131).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1581 include Ceres CLONE ID no. 1887320 (SEQ ID NO:2143) and Ceres ANNOT ID no. 6009958 (SEQ ID NO:2174).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:939-941, SEQ ID NO:943, SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NOs:2068-2083, SEQ ID NO:2131, SEQ ID NO:2143, SEQ ID NO:2174, SEQ ID NO:2330, or SEQ ID NO:2332.

A regulatory protein can contain a GRP domain characteristic of a polypeptide belonging to the glycine-rich protein family. This family of polypeptides includes several glycine-rich proteins as well as nodulins 16 and 24. The family also contains polypeptides that are induced in response to various stresses. Some of the polypeptides that have a glycine-rich domain (i.e., GRPs) are capable of binding to RNA, potentially affecting the stability and translatability of bound RNAs. SEQ ID NO:372, SEQ ID NO:1185, SEQ ID NO:1393, and SEQ ID NO:1846 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 113443 (SEQ ID NO:371), Ceres CLONE ID no. 3929 (SEQ ID NO:1184), Ceres CLONE ID no. 118184 (SEQ ID NO:1392), and Ceres CLONE ID no. 207629 (SEQ ID NO:1845), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a GRP domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:372, SEQ ID NO:1185, SEQ ID NO:1393, or SEQ ID NO:1846. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:372, SEQ ID NO:1185, SEQ ID NO:1393, or SEQ ID NO:1846. For example, a regulatory protein can have an amino acid sequence with at least 55% sequence identity, e.g., 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:372, SEQ ID NO:1185, SEQ ID NO:1393, or SEQ ID NO:1846.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1185 are provided in FIG. 71.

For example, the alignment in FIG. 71 provides the amino acid sequences of cDNA ID 23389966 (Ceres CLONE ID no. 3929; SEQ ID NO:1185), gi|20197615 (SEQ ID NO:1187), CeresClone:18215 (SEQ ID NO:1188), CeresClone:105261 (SEQ ID NO:1190), CeresClone:24667 (SEQ ID NO:1193), CeresClone:118878 (SEQ ID NO:1195), CeresClone:12459 (SEQ ID NO:1196), and CeresClone:1354021 (SEQ ID NO:1197). Other homologs and/or orthologs of SEQ ID NO:1185 include Ceres cDNA ID no. 23389966 (SEQ ID NO:1186), Public GI no. 21536606 (SEQ ID NO:1189), Ceres CLONE ID no. 23214 (SEQ ID NO:1191), Ceres CLONE ID no. 207629 (SEQ ID NO:1192), Ceres CLONE ID no. 1006473 (SEQ ID NO:1194), Public GI no. 30017217 (SEQ ID NO:1198), Ceres CLONE ID no. 109026 (SEQ ID NO:1199), SEQ ID NO:1200, Ceres CLONE ID no. 118184 (SEQ ID NO:1201), Ceres CLONE ID no. 118878 (SEQ ID NO:1202), Ceres CLONE ID no. 12459 (SEQ ID NO:1203), Ceres CLONE ID no. 1354021 (SEQ ID NO:1204), Public GI no. 30017217 (SEQ ID NO:1205), Ceres CLONE ID no. 109026 (SEQ ID NO:1206), Public GI no. 1252961811 (SEQ ID NO:1207), and Ceres CLONE ID no. 1767187 (SEQ ID NO:1209).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:1186-1207, or SEQ ID NO:1209.

A regulatory protein can contain a Usp domain characteristic of a polypeptide belonging to the universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial polypeptide whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general “stress endurance” activity. SEQ ID NO:1096 and SEQ ID NO:1862 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 7774 (SEQ ID NO:1095) and Ceres CLONE ID no. 2767 (SEQ ID NO:1861), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a Usp domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1096 or SEQ ID NO:1862. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1096 or SEQ ID NO:1862. For example, a regulatory protein can have an amino acid sequence with at least 55% sequence identity, e.g., 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1096 or SEQ ID NO:1862.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1096 are provided in FIG. 66.

For example, the alignment in FIG. 66 provides the amino acid sequences of Ceres Clone 7774 (SEQ ID NO:1096), 1449565 (SEQ ID NO:1098), gi|92875130 (SEQ ID NO:1099), CeresClone:1728645 (SEQ ID NO:1100), CeresClone:892214 (SEQ ID NO:1101), and gi|50913251 (SEQ ID NO:1102).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:1098-1102.

A regulatory protein can contain a GASA domain characteristic of a polypeptide belonging to the GASA gibberellin regulated cysteine rich protein family. The expression of these polypeptides is up-regulated by the plant hormone gibberellin. Most of these gibberellin regulated polypeptides have a role in plant development. There are 12 conserved cysteine residues, making it possible for these proteins to possess six disulphide bonds. SEQ ID NO:548 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 1845 (SEQ ID NO:547), that is predicted to encode a Pfam domain as indicated in the Sequence Listing (e.g., a gibberellin regulated polypeptide).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:548. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:548. For example, a regulatory protein can have an amino acid sequence with at least 50% sequence identity, e.g., 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:548.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:548 are provided in FIG. 26.

For example, the alignment in FIG. 26 provides the amino acid sequences of Ceres Clone 1845 (SEQ ID NO:548), CeresClone:890211 (SEQ ID NO:549), CeresClone:556120 (SEQ ID NO:550), and CeresAnnot:1483577 (SEQ ID NO:553). Other homologs and/or orthologs of SEQ ID NO:548 include Ceres CLONE ID no. 1618178 (SEQ ID NO:551).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:549-551 or SEQ ID NO:553.

A regulatory protein can contain one or more tetratricopeptide repeats (TPRs). For example, a regulatory protein can contain a TPR_(—)2 motif. Tetratricopeptide repeats, such as TPR_(—)1, TPR_(—)2, TPR_(—)3, and TPR_(—)4, are structural motifs that are present in a wide range of polypeptides and that mediate polypeptide-polypeptide interactions and assembly of multi-polypeptide complexes. The TPR motif consists of 316 tandem repeats of 34 amino acid residues, although individual TPR motifs can be dispersed in the polypeptide sequence. Sequence alignment of TPR domains has revealed a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Polypeptides containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis, and protein folding. SEQ ID NO:1421 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 13930 (SEQ ID NO:1420), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a TPR_(—)2 motif).

In some cases, a regulatory protein can contain a TPR_(—)1 motif and a TPR_(—)2 motif. SEQ ID NO:781, SEQ ID NO:964, and SEQ ID NO:1897 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 36370 (SEQ ID NO:780), Ceres CLONE ID no. 539801 (SEQ ID NO:963), and Ceres CLONE ID no. 5398 (SEQ ID NO:1896), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a TPR_(—)1 motif and a TPR_(—)2 motif).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1421, SEQ ID NO:781, SEQ ID NO:964, or SEQ ID NO:1897. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1421, SEQ ID NO:781, SEQ ID NO:964, or SEQ ID NO:1897. For example, a regulatory protein can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1421, SEQ ID NO:781, SEQ ID NO:964, or SEQ ID NO:1897.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:781, SEQ ID NO:964, and SEQ ID NO:1897 are provided in FIG. 48, FIG. 60, and FIG. 130, respectively.

For example, the alignment in FIG. 48 provides the amino acid sequences of Ceres Clone 36370 (SEQ ID NO:781), CeresClone:627169 (SEQ ID NO:784), CeresClone:1724787 (SEQ ID NO:786), gi|34914598 (SEQ ID NO:787), CeresClone:1397168 (SEQ ID NO:788), CeresAnnot:1481678 (SEQ ID NO:790), and CeresClone:704527 (SEQ ID NO:791). Other homologs and/or orthologs of SEQ ID NO:781 include Public GI no. 18400278 (SEQ ID NO:782) and Public GI no. 9294636 (SEQ ID NO:783).

The alignment in FIG. 60 provides the amino acid sequences of Ceres Clone 539801 (SEQ ID NO:964), CeresAnnot:1531585 (SEQ ID NO:966), CeresClone:1209672 (SEQ ID NO:969), and gi|51090847 (SEQ ID NO:971). Other homologs and/or orthologs of SEQ ID NO:964 include Ceres ANNOT ID no. 1537203 (SEQ ID NO:968), Public GI no. 21304447 (SEQ ID NO:970), Ceres ANNOT ID no. 1531585 (SEQ ID NO:973), Ceres ANNOT ID no. 1537203 (SEQ ID NO:975), Ceres CLONE ID no. 1209672 (SEQ ID NO:976), Public GI no. 21304447 (SEQ ID NO:977), Public GI no. 51090847 (SEQ ID NO:978), Ceres ANNOT ID no. 6017514 (SEQ ID NO:2212), and Ceres ANNOT ID no. 6054789 (SEQ ID NO:2284).

The alignment in FIG. 130 provides the amino acid sequences of CeresClone:5398 (SEQ ID NO:1897), CeresClone:1836567 (SEQ ID NO:1899), 1458988 (SEQ ID NO:1901), and gi|92899044 (SEQ ID NO:1902). Other homologs and/or orthologs of SEQ ID NO:1897 include Ceres ANNOT ID no. 6017514 (SEQ ID NO:2210) and Ceres ANNOT ID no. 6054789 (SEQ ID NO:2282).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:782-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2282, or SEQ ID NO:2284.

A regulatory protein can contain a Response_reg domain. The response regulator receiver domain, which belongs to the CheY family, receives the signal from the sensor partner in the two-component system. The response regulator polypeptides act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these polypeptides consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. SEQ ID NO:1698 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 968026 (SEQ ID NO:1697), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a Response_reg domain).

In some cases, a regulatory protein can contain a Response_reg domain and a myb-like DNA binding domain described above. SEQ ID NO:898 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 41875 (SEQ ID NO:897), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a Response_reg domain and a myb-like DNA binding domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:1698 or SEQ ID NO:898. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1698 or SEQ ID NO:898. For example, a regulatory protein can have an amino acid sequence with at least 50% sequence identity, e.g., 50%, 55%, 60%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1698 or SEQ ID NO:898.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1698 are provided in FIG. 118.

For example, the alignment in FIG. 118 provides the amino acid sequences of ME05220 (Ceres CLONE ID no. 968026; SEQ ID NO:1698), CeresClone:596510 (SEQ ID NO:2057) and gi|28466913 (SEQ ID NO:2056). Other homologs and/or orthologs of SEQ ID NO:1698 include Public GI No. 4678318 (SEQ ID NO:1975), Ceres ANNOT ID no. 1473516 (SEQ ID NO:1700), Ceres ANNOT ID no. 1526929 (SEQ ID NO:1702), Ceres ANNOT ID no. 1513366 (SEQ ID NO:1704), Ceres ANNOT ID no. 1460097 (SEQ ID NO:1706), Ceres ANNOT ID no. 1459838 (SEQ ID NO:1708), Ceres ANNOT ID no. 1474764 (SEQ ID NO:1710), Ceres ANNOT ID no. 1453555 (SEQ ID NO:1712), Ceres ANNOT ID no. 1448253 (SEQ ID NO:1714), Ceres ANNOT ID no. 1437849 (SEQ ID NO:1716), Ceres ANNOT ID no. 1443270 (SEQ ID NO:1718), and Ceres ANNOT ID no. 1496190 (SEQ ID NO:1720).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:2056-2057, SEQ ID NO:1975, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710, SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, or SEQ ID NO:1720.

A regulatory protein can contain a Ras domain characteristic of a Ras family polypeptide. Most of the members of the Ras superfamily have GTPase activity and some of the members have been implicated in various processes including cell development, cell and tissue differentiation, growth, survival, cytokine production, and vesicle-trafficking. The small Ras-GTPases are involved in intracellular cell signaling transduction pathway leading to modulation of gene expression, thus affecting the various processes mentioned above. SEQ ID NO:652, SEQ ID NO:1267, and SEQ ID NO:1888 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 2898 (SEQ ID NO:651), Ceres CLONE ID no. 34414 (SEQ ID NO:1266), and Ceres CLONE ID no. 6827 (SEQ ID NO:1887), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a Ras domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:652, SEQ ID NO:1267, or SEQ ID NO:1888. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:652, SEQ ID NO:1267, or SEQ ID NO:1888. For example, a regulatory protein can have an amino acid sequence with at least 65% sequence identity, e.g., 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:652, SEQ ID NO:1267, or SEQ ID NO:1888.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:652 and SEQ ID NO:1267 are provided in FIG. 34 and FIG. 76, respectively.

For example, the alignment in FIG. 34 provides the amino acid sequences of Ceres Clone 2898 (SEQ ID NO:652), CeresClone:1716210 (SEQ ID NO:653), CeresClone:1421639 (SEQ ID NO:654), 1443201 (SEQ ID NO:656), CeresClone:749118 (SEQ ID NO:657), and 1450718 (SEQ ID NO:659). Other homologs and/or orthologs of SEQ ID NO:652 include Ceres ANNOT ID no. 1450718 (SEQ ID NO:2091) and Ceres CLONE ID no. 1956018 (SEQ ID NO:2155).

The alignment in FIG. 76 provides the amino acid sequences of cDNA ID 23384563 (Ceres CLONE ID no. 34414; SEQ ID NO:1267), CeresClone:14909 (SEQ ID NO:1986), CeresClone:1535974 (SEQ ID NO:1991), CeresClone:276776 (SEQ ID NO:1990), CeresClone:240510 (SEQ ID NO:1992), gi|39653273 (SEQ ID NO:1989), CeresClone:33126 (SEQ ID NO:1987), and CeresClone:1338585 (SEQ ID NO:1988). Other homologs and/or orthologs of SEQ ID NO:1267 include Ceres ANNOT ID no. 1471525 (SEQ ID NO:1269), Ceres ANNOT ID no. 1497838 (SEQ ID NO:1271), Ceres ANNOT ID no. 1511908 (SEQ ID NO:1273), Ceres ANNOT ID no. 1464305 (SEQ ID NO:1275), Ceres ANNOT ID no. 1451416 (SEQ ID NO:1277), Ceres ANNOT ID no. 1514324 (SEQ ID NO:1279), Ceres ANNOT ID no. 1461050 (SEQ ID NO:1281), and Ceres CLONE ID no. 1724996 (SEQ ID NO:1283).

Amino acid sequence of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1888 include Ceres ANNOT ID no. 1453294 (SEQ ID NO:2099) and Ceres ANNOT ID no. 6087117 (SEQ ID NO:2318).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:653-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1986-1992, SEQ ID NO:2091, SEQ ID NO:2099, SEQ ID NO:2155, or SEQ ID NO:2318.

A regulatory protein can contain an MMR_HSR1 domain characteristic of a GTPase polypeptide belonging to a subfamily of GTP-binding polypeptides. Polypeptides representing this subfamily include human HSR1, which has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1, from mouse. SEQ ID NO:585 and SEQ ID NO:1890 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 224919 (SEQ ID NO:584) and Ceres CLONE ID no. 969682 (SEQ ID NO:1889), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an MMR_HSR1 domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:585 or SEQ ID NO:1890. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:585 or SEQ ID NO:1890. For example, a regulatory protein can have an amino acid sequence with at least 80% sequence identity, e.g., 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:585 or SEQ ID NO:1890.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:585 are provided in FIG. 29. Other homologs and/or orthologs of SEQ ID NO:585 include Ceres CLONE ID no. 1963936 (SEQ ID NO:2129).

For example, the alignment in FIG. 29 provides the amino acid sequences of Ceres Clone 224919 (SEQ ID NO:585), gi|50933495 (SEQ ID NO:586) and CeresClone:1556085 (SEQ ID NO:587). Other homologs and/or orthologs of SEQ ID NO:585 include Public GI no. 218204 (SEQ ID NO:588).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1890 include Ceres ANNOT ID no. 1475363 (SEQ ID NO:2107).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:586-588, SEQ ID NO:2107, or SEQ ID NO:2129.

A regulatory protein can contain a Ras domain and an MMR_HSR1 domain, both of which are described above. SEQ ID NO:465 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 1492 (SEQ ID NO:464), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a Ras domain and an MMR_HSR1 domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:465. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:465. For example, a regulatory protein can have an amino acid sequence with at least 75% sequence identity, e.g., 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:465.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:465 are provided in FIG. 20.

For example, the alignment in FIG. 20 provides the amino acid sequences of CeresClone:1492 (SEQ ID NO:465), gi|89257443 (SEQ ID NO:466), CeresClone:1128644 (SEQ ID NO:467), gi|4586580 (SEQ ID NO:468), CeresClone:1835140 (SEQ ID NO:470), gi|50911379 (SEQ ID NO:471), 1538756 (SEQ ID NO:473), CeresClone:1840642 (SEQ ID NO:475), gi|311907 (SEQ ID NO:476), CeresClone:1932400 (SEQ ID NO:478), gi|1053067 (SEQ ID NO:479), CeresClone:727613 (SEQ ID NO:480), gi|34914060 (SEQ ID NO:481), CeresClone:1834939 (SEQ ID NO:483), gi|2500073 (SEQ ID NO:484), gi|5902803 (SEQ ID NO:485), CeresClone:1785552 (SEQ ID NO:487), and gi|401686 (SEQ ID NO:488). Other homologs and/or orthologs of SEQ ID NO:465 include Ceres ANNOT ID no. 1539674 (SEQ ID NO:2117), Ceres CLONE ID no. 1771639 (SEQ ID NO:2123), and Ceres ANNOT ID no. 6052977 (SEQ ID NO:2280).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:466-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:2117, SEQ ID NO:2123, or SEQ ID NO:2280.

A regulatory protein can contain an Arf domain characteristic of polypeptides belonging to the ADP-ribosylation factor family. The small ADP ribosylation factor (Arf) GTP-binding polypeptides are major regulators of vesicle biogenesis in intracellular traffic. They are the founding members of a growing family that includes Arl (Arf-like), Arp (Arf-related proteins), and the remotely related Sar (Secretion-associated and Ras-related) polypeptides. Arf polypeptides cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. Members of the ADP-ribosylation factor family may indirectly affect transcription through polypeptide-polypeptide interactions. SEQ ID NO:686, SEQ ID NO:994, and SEQ ID NO:1211 set forth the amino acid sequences of DNA clones, identified herein as Ceres CLONE ID no. 312833 (SEQ ID NO:685), Ceres CLONE ID no. 543118 (SEQ ID NO:993), and Ceres CLONE ID no. 14909 (SEQ ID NO:1210), respectively, each of which is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., an Arf domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:686, SEQ ID NO:994, or SEQ ID NO:1211. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:686, SEQ ID NO:994, or SEQ ID NO:1211. For example, a regulatory protein can have an amino acid sequence with at least 60% sequence identity, e.g., 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:686, SEQ ID NO:994, or SEQ ID NO:1211.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:686, SEQ ID NO:994, and SEQ ID NO:1211 are provided in FIG. 38, FIG. 62, and FIG. 72, respectively.

For example, the alignment in FIG. 38 provides the amino acid sequences of Ceres Clone 312833 (SEQ ID NO:686) and gi|50920025 (SEQ ID NO:687). Other homologs and/or orthologs of SEQ ID NO:686 include Ceres ANNOT ID no. 6010155 (SEQ ID NO:2178).

The alignment in FIG. 62 provides the amino acid sequences of Ceres Clone 543118 (SEQ ID NO:994), gi|871508 (SEQ ID NO:995), gi|1370190 (SEQ ID NO:996), gi|1654144 (SEQ ID NO:998), gi|18447913 (SEQ ID NO:999), gi|92897911 (SEQ ID NO:1000), gi|28973447 (SEQ ID NO:1005), CeresAnnot:1458068 (SEQ ID NO:1007), CeresClone:636809 (SEQ ID NO:1008), CeresClone:1895506 (SEQ ID NO:1011), gi|974776 (SEQ ID NO:1019), gi|5669640 (SEQ ID NO:1020), CeresClone:1390343 (SEQ ID NO:1021), CeresClone:683923 (SEQ ID NO:1023), gi|313029 (SEQ ID NO:1024), CeresClone:1725800 (SEQ ID NO:1025), gi|2808638 (SEQ ID NO:1026), gi|50935375 (SEQ ID NO:1029), CeresClone:1802574 (SEQ ID NO:1031), and gi|549809 (SEQ ID NO:1048). Other homologs and/or orthologs of SEQ ID NO:994 include Public GI no. 871506 (SEQ ID NO:997), Public GI no. 18447921 (SEQ ID NO:1001), Public GI no. 871514 (SEQ ID NO:1002), Public GI no. 1370194 (SEQ ID NO:1003), Public GI no. 18447917 (SEQ ID NO:1004), Public GI no. 18447919 (SEQ ID NO:1009), Public GI no. 14334918 (SEQ ID NO:1012), Public GI no. 871510 (SEQ ID NO:1013), Ceres CLONE ID no. 256151 (SEQ ID NO:1014), Ceres ANNOT ID no. 1461863 (SEQ ID NO:1016), Public GI no. 1370196 (SEQ ID NO:1017), Public GI no. 1370198 (SEQ ID NO:1018), Public GI no. 21555222 (SEQ ID NO:1022), Ceres CLONE ID no. 1851155 (SEQ ID NO:1028), Public GI no. 50919469 (SEQ ID NO:1032), Ceres CLONE ID no. 1281221 (SEQ ID NO:1033), Ceres CLONE ID no. 1724467 (SEQ ID NO:1035), Ceres CLONE ID no. 1076158 (SEQ ID NO:1036), Ceres CLONE ID no. 689414 (SEQ ID NO:1037), Ceres CLONE ID no. 1290569 (SEQ ID NO:1038), Ceres CLONE ID no. 1021031 (SEQ ID NO:1039), Public GI no. 50931689 (SEQ ID NO:1040), Ceres CLONE ID no. 239853 (SEQ ID NO:1041), Public GI no. 46326983 (SEQ ID NO:1042), Public GI no. 15810625 (SEQ ID NO:1043), Public GI no. 21592670 (SEQ ID NO:1044), Ceres CLONE ID no. 3115 (SEQ ID NO:1045), Public GI no. 6681329 (SEQ ID NO:1046), Ceres CLONE ID no. 10506 (SEQ ID NO:1047), Ceres ANNOT ID no. 6011078 (SEQ ID NO:2180), and Ceres ANNOT ID no. 6039802 (SEQ ID NO:2264).

The alignment in FIG. 72 provides the amino acid sequences of Ceres Clone 14909 (SEQ ID NO:1211), CeresClone:1561415 (SEQ ID NO:1226), CeresClone:380874 (SEQ ID NO:1227), CeresClone:416460 (SEQ ID NO:1228), CeresClone:631823 (SEQ ID NO:1229), CeresClone:1535974 (SEQ ID NO:1230), CeresClone:1428788 (SEQ ID NO:1231), CeresClone:738726 (SEQ ID NO:1232), CeresClone:276776 (SEQ ID NO:1233), CeresClone:240510 (SEQ ID NO:1234), and CeresClone:529239 (SEQ ID NO:1235). Other homologs and/or orthologs of SEQ ID NO:1211 include Ceres ANNOT ID no. 1497838 (SEQ ID NO:1213), Ceres ANNOT ID no. 1522523 (SEQ ID NO:1215), Ceres ANNOT ID no. 1471525 (SEQ ID NO:1217), Ceres ANNOT ID no. 1511908 (SEQ ID NO:1219), Ceres ANNOT ID no. 1464305 (SEQ ID NO:1221), Ceres ANNOT ID no. 1451416 (SEQ ID NO:1223), Ceres ANNOT ID no. 1461050 (SEQ ID NO:1225), Ceres CLONE ID no. 1724996 (SEQ ID NO:1237), and Ceres ANNOT ID no. 6085974 (SEQ ID NO:2310).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:687, SEQ ID NOs:995-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2264, or SEQ ID NO:2310.

A regulatory protein can contain a PsbP domain. The PsbP polypeptide family consists of the 23 kDa subunit of oxygen evolving system of photosystem II or PsbP from various plants, where it is encoded by the nuclear genome, and cyanobacteria. Both PsbP and PsbQ are regulators that are necessary for the biogenesis of optically active PSII. The 23 KDa PsbP polypeptide is required for PSII to be fully operational in vivo. PsbP increases the affinity of the water oxidation site for chloride ions and provides the conditions required for high affinity binding of calcium ions. SEQ ID NO:1906 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 9325 (SEQ ID NO:1905), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a PsbP domain).

A regulatory protein can comprise the amino acid sequence set forth SEQ ID NO:1906. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1906. For example, a regulatory protein can have an amino acid sequence with at least 30% sequence identity, e.g., 31%, 35%, 40%, 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1906.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1906 are provided in FIG. 131.

For example, the alignment in FIG. 131 provides the amino acid sequences of cDNA ID 23367406 (Ceres CLONE ID no. 9325; SEQ ID NO:1906), gi|7443216, CeresClone:982579 (SEQ ID NO:2045), gi|11133887 (SEQ ID NO:2041), CeresClone:1139782 (SEQ ID NO:2042), gi|42569485 (SEQ ID NO:2044), gi|21133 (SEQ ID NO:2040), CeresClone:1063835 (SEQ ID NO:2038), CeresClone:1027529 (SEQ ID NO:2039), and CeresClone:142681 (SEQ ID NO:2037). Other homologs and/or orthologs of SEQ ID NO:1906 include Ceres ANNOT ID no. 1461478 (SEQ ID NO:1908), Public GI no. 2880056 (SEQ ID NO:2043), Ceres ANNOT ID no. 1442982 (SEQ ID NO:2089), and Ceres CLONE ID no. 1756586 (SEQ ID NO:2119).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:1908, SEQ ID NOs:2037-2045, SEQ ID NO:2089, SEQ ID NO:2119, or gi|7443216.

A regulatory protein can have a PRK domain characteristic of polypeptides belonging to the phosphoribulokinase/uridine kinase family. Phosphoribulokinase (PRK) catalyzes the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. SEQ ID NO:744 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 339518 (SEQ ID NO:743), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a PRK domain).

A regulatory protein can comprise the amino acid sequence set forth SEQ ID NO:744. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:744. For example, a regulatory protein can have an amino acid sequence with at least 70% sequence identity, e.g., 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:744.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:744 are provided in FIG. 46.

For example, the alignment in FIG. 46 provides the amino acid sequences of Ceres Clone 339518 (SEQ ID NO:744), CeresClone:243130 (SEQ ID NO:745), CeresClone:1776411 (SEQ ID NO:747), gi|50911777 (SEQ ID NO:748), gi|100796 (SEQ ID NO:750), CeresAnnot:1500106 (SEQ ID NO:753), gi|23197622 (SEQ ID NO:756), and gi|21279 (SEQ ID NO:758). Other homologs and/or orthologs of SEQ ID NO:744 include Public GI no. 5924030 (SEQ ID NO:749), Public GI no. 21839 (SEQ ID NO:751), Ceres ANNOT ID no. 1539024 (SEQ ID NO:755), and Ceres CLONE ID no. 11226 (SEQ ID NO:757).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:745, SEQ ID NOs:747-751, SEQ ID NO:753, or SEQ ID NOs:755-758.

A regulatory protein can have a DLH domain characteristic of a polypeptide belonging to the dienelactone hydrolase family. Dienelactone hydrolases play a crucial role in chlorocatechol degradation via the modified ortho cleavage pathway. Enzymes induced in 4-fluorobenzoate-utilizing bacteria have been classified into three groups based on their specificity towards cis- and trans-dienelactone. Some polypeptides, such as the rat kan-1 polypeptide, contain repeated small fragments of the DLH domain. SEQ ID NO:1876 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 520515 (SEQ ID NO:1875), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a DLH domain).

A regulatory protein can comprise the amino acid sequence set forth SEQ ID NO:1876. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1876. For example, a regulatory protein can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1876.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1876 include Ceres ANNOT ID no. 1450854 (SEQ ID NO:2093).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:2093.

A regulatory protein can have a PDT domain found in prephenate dehydratase polypeptides. Prephenate dehydratase polypeptides catalyze the decarboxylation of prephenate to phenylpyruvate. In microorganisms, the prephenate dehydratase polypeptide is part of the terminal pathway of phenylalanine biosynthesis. In some bacteria, such as Escherichia coli, the PDT domain is included in a bifunctional enzyme, P-protein, that also catalyzes the transformation of chorismate into prephenate. In other bacteria, prephenate dehydratase enzymes occur as monofunctional polypeptides. The sequence of monofunctional prephenate dehydratase aligns well with the C-terminal part of P-proteins. SEQ ID NO:793 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 37739 (SEQ ID NO:792), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a PDT domain).

A regulatory protein can comprise the amino acid sequence set forth SEQ ID NO:793. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:793. For example, a regulatory protein can have an amino acid sequence with at least 65% sequence identity, e.g., 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:793.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:793 are provided in FIG. 49.

For example, the alignment in FIG. 49 provides the amino acid sequences of Ceres Clone 37739 (SEQ ID NO:793), gi|20259555 (SEQ ID NO:794), CeresClone:1754197 (SEQ ID NO:796), CeresClone:1856164 (SEQ ID NO:798), 1488340 (SEQ ID NO:800), CeresClone:1807870 (SEQ ID NO:802), gi|45935145 (SEQ ID NO:803), CeresClone:383227 (SEQ ID NO:804), gi|70664005 (SEQ ID NO:805), and CeresClone:909699 (SEQ ID NO:806). Other homologs and/or orthologs of SEQ ID NO:793 include Ceres ANNOT ID no. 6030226 (SEQ ID NO:2238).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, or SEQ ID NO:2238.

A regulatory protein can contain a UDPGT domain characteristic of UDP-glucoronosyl and UDP-glucosyl transferase polypeptides. UDP glycosyltransferases (UGT) constitute a superfamily of enzymes that catalyze the addition of the glycosyl group from a UTP-sugar to a small hydrophobic molecule. Members of this family from plants include the flavonol O(3)-glucosyltransferase enzyme, which catalyzes the transfer of glucose from UDP-glucose to a flavanol. This reaction is one of the last steps in anthocyanin pigment biosynthesis. SEQ ID NO:914 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 479006 (SEQ ID NO:913), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a UDPGT domain).

A regulatory protein can comprise the amino acid sequence set forth SEQ ID NO:914. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:914. For example, a regulatory protein can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:914.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:914 are provided in FIG. 58.

For example, the alignment in FIG. 58 provides the amino acid sequences of Ceres Clone 479006 (SEQ ID NO:914), CeresAnnot:1444387 (SEQ ID NO:917), CeresClone:1886347 (SEQ ID NO:919), gi|13508844 (SEQ ID NO:922), gi|14532902 (SEQ ID NO:923), CeresClone:1858581 (SEQ ID NO:927), CeresClone:630211 (SEQ ID NO:930), CeresClone:1534695 (SEQ ID NO:931), and gi|77551916 (SEQ ID NO:932). Other homologs and/or orthologs of SEQ ID NO:914 include Ceres CLONE ID no. 1054168 (SEQ ID NO:915), Ceres ANNOT ID no. 1471286 (SEQ ID NO:921), Ceres CLONE ID no. 1204 (SEQ ID NO:924), Public GI no. 2191136 (SEQ ID NO:925), and Ceres CLONE ID no. 1769251 (SEQ ID NO:929).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NO:915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, or SEQ ID NOs:929-932.

A regulatory protein can contain a ZIP domain characteristic of a ZIP Zinc transporter polypeptide. The ZIP family of polypeptides consists of zinc transport polypeptides and putative metal transporter polypeptides. Arabidopsis thaliana ZIP family polypeptides are expressed in roots in response to zinc deficiency, suggesting that they may transport zinc from the soil into the plant. SEQ ID NO:339 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 105162 (SEQ ID NO:338), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a ZIP domain).

A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:339. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:339. For example, a regulatory protein can have an amino acid sequence with at least 55% sequence identity, e.g., 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:339.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:339 are provided in FIG. 10.

For example, the alignment in FIG. 10 provides the amino acid sequences of CeresClone:105162 (SEQ ID NO:339), CeresClone:1853694 (SEQ ID NO:343), CeresAnnot:1494468 (SEQ ID NO:345), gi|38036140 (SEQ ID NO:348), CeresClone:1649800 (SEQ ID NO:349), CeresClone:984060 (SEQ ID NO:350), gi|31872116 (SEQ ID NO:351), and CeresClone:1816624 (SEQ ID NO:353). Other homologs and/or orthologs of SEQ ID NO:339 include Public GI no. 20147287 (SEQ ID NO:340), Public GI no. 8778308 (SEQ ID NO:341), and Ceres ANNOT ID no. 1441572 (SEQ ID NO:347).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:340-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NOs:347-351, or SEQ ID NO:353.

A regulatory protein can have a UPF0060 domain characteristic of polypeptides belonging to the uncharacterized BCR, YnfA/UPF0060 family of integral membrane polypeptides. SEQ ID NO:159 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres ANNOT ID no. 574716 (SEQ ID NO:158), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a UPF0060 domain).

A regulatory protein can comprise the amino acid sequence set forth SEQ ID NO:159. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:159. For example, a regulatory protein can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 47%, 48%, 49%, 50%, 51%, 52%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:159.

A regulatory protein can have a DUF298 domain. Members of the DUF298 polypeptide family contain a basic helix-loop-helix leucine zipper motif. The DUF298 domain is implicated in some aspect of neddylation of the cullin 3 family and has a possible role in the regulation of the polypeptide modifier Nedd8 E3 ligase. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a polypeptide through an isopeptide bond. SEQ ID NO:900 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 478453 (SEQ ID NO:899), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a DUF298 domain).

A regulatory protein can comprise the amino acid sequence set forth SEQ ID NO:900. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:900. For example, a regulatory protein can have an amino acid sequence with at least 65% sequence identity, e.g., 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:900.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:900 are provided in FIG. 57.

For example, the alignment in FIG. 57 provides the amino acid sequences of Ceres Clone 478453 (SEQ ID NO:900), CeresClone:1923578 (SEQ ID NO:904), gi|51535194 (SEQ ID NO:905), CeresClone:1956222 (SEQ ID NO:907), CeresClone:291139 (SEQ ID NO:908), and CeresClone:569584 (SEQ ID NO:910). Other homologs and/or orthologs of SEQ ID NO:900 include SEQ ID NO:901, Ceres CLONE ID no. 480964 (SEQ ID NO:902), Ceres CLONE ID no. 689194 (SEQ ID NO:909), Ceres CLONE ID no. 1724040 (SEQ ID NO:912), Ceres ANNOT ID no. 1458456 (SEQ ID NO:2103), Ceres ANNOT ID no. 6086494 (SEQ ID NO:2312), and Ceres ANNOT ID no. 6087143 (SEQ ID NO:2320).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:901-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NO:2103, SEQ ID NO:2312, or SEQ ID NO:2320.

A regulatory protein can have a DUF1313 domain characteristic of members of a polypeptide family comprising several hypothetical plant polypeptides of about 100 residues in length. SEQ ID NO:1585 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 397320 (SEQ ID NO:1584), that is predicted to encode a polypeptide containing a Pfam domain as indicated in the Sequence Listing (e.g., a DUF1313 domain).

A regulatory protein can comprise the amino acid sequence set forth SEQ ID NO:1585. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1585. For example, a regulatory protein can have an amino acid sequence with at least 55% sequence identity, e.g., 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:1585.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1585 are provided in FIG. 107.

For example, the alignment in FIG. 107 provides the amino acid sequences of cDNA ID 23814706 (Ceres CLONE ID no. 397320; SEQ ID NO:1585), gi|37991859 (SEQ ID NO:2055), CeresClone:327449 (SEQ ID NO:2054), CeresClone:476445 (SEQ ID NO:2053), CeresClone:1066463 (SEQ ID NO:2052), CeresClone:1349 (SEQ ID NO:2046), and CeresClone:1099781 (SEQ ID NO:2051). Other homologs and/or orthologs of SEQ ID NO:1585 include Ceres ANNOT ID no. 1484716 (SEQ ID NO:1587), Ceres ANNOT ID no. 1499354 (SEQ ID NO:1589), Ceres ANNOT ID no. 1491719 (SEQ ID NO:1591), Ceres ANNOT ID no. 1533409 (SEQ ID NO:1593), Public GI no. 62318582 (SEQ ID NO:2047), Public GI no. 8778455 (SEQ ID NO:2048), Ceres CLONE ID no. 19640 (SEQ ID NO:2049), Public GI no. 19310623 (SEQ ID NO:2050), and Ceres CLONE ID no. 1958407 (SEQ ID NO:2157).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:2046-2055, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, or SEQ ID NO:2157.

A regulatory protein can have a Lipoxygenase domain and a PLAT domain. Lipoxygenases are a class of iron-containing dioxygenases that catalyze the hydroperoxidation of lipids containing a cis,cis-1,4-pentadiene structure. Lipoxygenases are common in plants, where they may be involved in diverse aspects of plant physiology including growth and development, pest resistance, and senescence or responses to wounding. The PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain, or LH2 (Lipoxygenase homology) domain, is found in a variety of membrane or lipid associated polypeptides, such as lipogenase enzymes that are involved at various steps in the biosynthesis of leukotrienes and use iron as the cofactor. The PLAT domain has a beta sandwich structure and may mediate membrane attachment via other protein binding partners. SEQ ID NO:2085 sets forth the amino acid sequence of a DNA clone, identified herein as Ceres CLONE ID no. 362993 (SEQ ID NO:2084), that is predicted to encode a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a Lipoxygenase domain and a PLAT domain).

A regulatory protein can comprise the amino acid sequence set forth SEQ ID NO:2085. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:2085. For example, a regulatory protein can have an amino acid sequence with at least 40% sequence identity, e.g., 45%, 50%, 56%, 57%, 60%, 61%, 62%, 63%, 64%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:2085.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:2085 include Ceres ANNOT ID no. 6016572 (SEQ ID NO:2202) and Ceres ANNOT ID no. 6016579 (SEQ ID NO:2204).

SEQ ID NO:96, SEQ ID NO:104, SEQ ID NO:157, SEQ ID NO:337, SEQ ID NO:357, SEQ ID NO:407, SEQ ID NO:415, SEQ ID NO:438, SEQ ID NO:520, SEQ ID NO:524, SEQ ID NO:610, SEQ ID NO:638, SEQ ID NO:678, SEQ ID NO:730, SEQ ID NO:737, SEQ ID NO:838, SEQ ID NO:936, SEQ ID NO:1050, SEQ ID NO:1414, SEQ ID NO:1436, SEQ ID NO:1824, SEQ ID NO:1848, SEQ ID NO:1868, and SEQ ID NO:1880 set forth the amino acid sequences of DNA clones, identified herein as Ceres ANNOT ID no. 541887 (SEQ ID NO:95), Ceres ANNOT ID no. 542746 (SEQ ID NO:103), Ceres ANNOT ID no. 568299 (SEQ ID NO:156), Ceres CLONE ID no. 104839 (SEQ ID NO:336), Ceres CLONE ID no. 110428 (SEQ ID NO:356), Ceres CLONE ID no. 117643 (SEQ ID NO:406), Ceres CLONE ID no. 119790 (SEQ ID NO:414), Ceres CLONE ID no. 125917 (SEQ ID NO:437), Ceres CLONE ID no. 158240 (SEQ ID NO:519), Ceres CLONE ID no. 15990 (SEQ ID NO:523), Ceres CLONE ID no. 25816 (SEQ ID NO:609), Ceres CLONE ID no. 285598 (SEQ ID NO:637), Ceres CLONE ID no. 299144 (SEQ ID NO:677), Ceres CLONE ID no. 33435 (SEQ ID NO:729), Ceres CLONE ID no. 337432 (SEQ ID NO:736), Ceres CLONE ID no. 3900 (SEQ ID NO:837), Ceres CLONE ID no. 531573 (SEQ ID NO:935), Ceres CLONE ID no. 545182 (SEQ ID NO:1049), Ceres CLONE ID no. 12997 (SEQ ID NO:1413), Ceres CLONE ID no. 149496 (SEQ ID NO:1435), Ceres ANNOT ID no. 543489 (SEQ ID NO:1823), Ceres CLONE ID no. 21674 (SEQ ID NO:1847), Ceres CLONE ID no. 284030 (SEQ ID NO:1867), and Ceres CLONE ID no. 560898 (SEQ ID NO:1879), respectively, each of which is predicted to encode a polypeptide that does not have homology to an existing polypeptide family based on Pfam analysis or encodes a polypeptide having a Pfam domain as indicated in the Sequence Listing (e.g., a zf-C3HC4 domain, a tetratricopeptide motif, an AP2 domain, a zf-CCCH domain, or an ACT domain). A regulatory protein can comprise the amino acid sequence set forth in SEQ ID NO:96, SEQ ID NO:104, SEQ ID NO:157, SEQ ID NO:337, SEQ ID NO:357, SEQ ID NO:407, SEQ ID NO:415, SEQ ID NO:438, SEQ ID NO:520, SEQ ID NO:524, SEQ ID NO:610, SEQ ID NO:638, SEQ ID NO:678, SEQ ID NO:730, SEQ ID NO:737, SEQ ID NO:838, SEQ ID NO:936, SEQ ID NO:1050, SEQ ID NO:1414, SEQ ID NO:1436, SEQ ID NO:1824, SEQ ID NO:1848, SEQ ID NO:1868, or SEQ ID NO:1880. In some cases, a regulatory protein can be a homolog, ortholog, or variant of the polypeptide having the amino acid sequence set forth in SEQ ID NO:96, SEQ ID NO:104, SEQ ID NO:157, SEQ ID NO:337, SEQ ID NO:357, SEQ ID NO:407, SEQ ID NO:415, SEQ ID NO:438, SEQ ID NO:520, SEQ ID NO:524, SEQ ID NO:610, SEQ ID NO:638, SEQ ID NO:678, SEQ ID NO:730, SEQ ID NO:737, SEQ ID NO:838, SEQ ID NO:936, SEQ ID NO:1050, SEQ ID NO:1414, SEQ ID NO:1436, SEQ ID NO:1824, SEQ ID NO:1848, SEQ ID NO:1868, or SEQ ID NO:1880. For example, a regulatory polypeptide can have an amino acid sequence with at least 30% sequence identity, e.g., 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence set forth in SEQ ID NO:96, SEQ ID NO:104, SEQ ID NO:157, SEQ ID NO:337, SEQ ID NO:357, SEQ ID NO:407, SEQ ID NO:415, SEQ ID NO:438, SEQ ID NO:520, SEQ ID NO:524, SEQ ID NO:610, SEQ ID NO:638, SEQ ID NO:678, SEQ ID NO:730, SEQ ID NO:737, SEQ ID NO:838, SEQ ID NO:936, SEQ ID NO:1050, SEQ ID NO:1414, SEQ ID NO:1436, SEQ ID NO:1824, SEQ ID NO:1848, SEQ ID NO:1868, or SEQ ID NO:1880.

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:96, SEQ ID NO:357, SEQ ID NO:438, SEQ ID NO:520, SEQ ID NO:638, SEQ ID NO:730, SEQ ID NO:737, SEQ ID NO:838, SEQ ID NO:1414, and SEQ ID NO:1436 are provided in FIG. 1, FIG. 11, FIG. 17, FIG. 23, FIG. 33, FIG. 44, FIG. 45, FIG. 53, FIG. 90, and FIG. 92, respectively.

For example, the alignment in FIG. 1 provides the amino acid sequences of Annot ID 541887 (SEQ ID NO:96), CeresAnnot:1448288 (SEQ ID NO:98), CeresClone:644583 (SEQ ID NO:99), gi|50926522 (SEQ ID NO:100), and CeresClone:1791381 (SEQ ID NO:102).

The alignment in FIG. 11 provides the amino acid sequences of CeresClone:110428 (SEQ ID NO:357) and CeresClone:1444428 (SEQ ID NO:359). Other homologs and/or orthologs of SEQ ID NO:357 include Public GI no. 11994473 (SEQ ID NO:358).

The alignment in FIG. 17 provides the amino acid sequences of CeresClone:125917 (SEQ ID NO:438), CeresAnnot:1456569 (SEQ ID NO:440), CeresAnnot:1450998 (SEQ ID NO:442), and gi|92873189 (SEQ ID NO:443).

The alignment in FIG. 23 provides the amino acid sequences of Ceres Clone 158240 (SEQ ID NO:520), gi|37538128 (SEQ ID NO:521) and gi|84453218 (SEQ ID NO:522). Other homologs and/or orthologs of SEQ ID NO:520 include Ceres ANNOT ID no. 6006556 (SEQ ID NO:2164), Ceres ANNOT ID no. 6067965 (SEQ ID NO:2298), and Ceres ANNOT ID no. 6086771 (SEQ ID NO:2314).

The alignment in FIG. 33 provides the amino acid sequences of Ceres Clone 285598 (SEQ ID NO:638), CeresClone:236111 (SEQ ID NO:639), gi|34902144 (SEQ ID NO:640), CeresClone:1315656 (SEQ ID NO:641), gi|45602841 (SEQ ID NO:642), gi|45544873 (SEQ ID NO:643), gi|45758663 (SEQ ID NO:644), gi|62320820 (SEQ ID NO:645), gi|92888885 (SEQ ID NO:647), gi|40807658 (SEQ ID NO:648), and CeresAnnot:1486505 (SEQ ID NO:650). Other homologs and/or orthologs of SEQ ID NO:638 include Ceres CLONE ID no. 1344853 (SEQ ID NO:646) and Ceres CLONE ID no. 1911944 (SEQ ID NO:2151).

The alignment in FIG. 44 provides the amino acid sequences of Ceres Clone 33435 (SEQ ID NO:730), CeresClone:116606 (SEQ ID NO:731), CeresClone:1079147 (SEQ ID NO:732), CeresClone:957098 (SEQ ID NO:733), CeresClone:1435704 (SEQ ID NO:734), and CeresClone:1496331 (SEQ ID NO:735).

The alignment in FIG. 45 provides the amino acid sequences of Ceres Clone 337432 (SEQ ID NO:737), gi|50925955 (SEQ ID NO:738), CeresClone:1619846 (SEQ ID NO:739), gi|27754217 (SEQ ID NO:740), and CeresAnnot:1509127 (SEQ ID NO:742). Other homologs and/or orthologs of SEQ ID NO:737 include Ceres ANNOT ID no. 6064740 (SEQ ID NO:2294).

The alignment in FIG. 53 provides the amino acid sequences of Ceres Clone 3900 (SEQ ID NO:838), CeresClone:158765 (SEQ ID NO:839), CeresClone:1839717 (SEQ ID NO:841), 1480628 (SEQ ID NO:843), gi|5669656 (SEQ ID NO:844), CeresClone:1329861 (SEQ ID NO:845), CeresClone:537752 (SEQ ID NO:846), CeresClone:1322549 (SEQ ID NO:847), 1533351 (SEQ ID NO:849), and CeresClone:282892 (SEQ ID NO:850). Other homologs and/or orthologs of SEQ ID NO:838 include Ceres ANNOT ID no. 6064763 (SEQ ID NO:2296).

The alignment in FIG. 90 provides the amino acid sequences of Ceres Clone 12997 (SEQ ID NO:1414) and CeresClone:465893 (SEQ ID NO:1415). Other homologs and/or orthologs of SEQ ID NO:1414 include Ceres ANNOT ID no. 1483367 (SEQ ID NO:1417) and Ceres ANNOT ID no. 1474088 (SEQ ID NO:1419).

The alignment in FIG. 92 provides the amino acid sequences of CeresClone:149496 (SEQ ID NO:1436), CeresClone:833872 (SEQ ID NO:1439) and CeresClone:1579587 (SEQ ID NO:1442). Other homologs and/or orthologs of SEQ ID NO:1436 include Public GI no. 5616313 (SEQ ID NO:1437), Ceres CLONE ID no. 751992 (SEQ ID NO:1438), Public GI no. 62901482 (SEQ ID NO:1440), and Public GI no. 34906988 (SEQ ID NO:1441).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1824 include Ceres ANNOT ID no. 1457646 (SEQ ID NO:2101).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:1868 include Ceres CLONE ID no. 1881892 (SEQ ID NO:2141).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:415 include Ceres ANNOT ID no. 6015893 (SEQ ID NO:2192).

Amino acid sequences of homologs and/or orthologs of the polypeptide having the amino acid sequence set forth in SEQ ID NO:524 include Ceres ANNOT ID no. 6016718 (SEQ ID NO:2206) and Ceres ANNOT ID no. 6041092 (SEQ ID NO:2272).

In some cases, a regulatory protein can include a polypeptide having at least 80% sequence identity, e.g., 80%, 85%, 90%, 93%, 95%, 97%, 98%, or 99% sequence identity, to an amino acid sequence corresponding to any of SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NOs:357-359, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NO:521-522, SEQ ID NOs:639-648, SEQ ID NO:650, SEQ ID NOs:731-735, SEQ ID NOs:738-740, SEQ ID NO:742, SEQ ID NO:839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NO:1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NOs:1437-1442, SEQ ID NO:2101, SEQ ID NO:2141, SEQ ID NO:2151, SEQ ID NO:2164, SEQ ID NO:2192, SEQ ID NO:2206, SEQ ID NO:2272, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, or SEQ ID NO:2314.

A regulatory protein encoded by a recombinant nucleic acid can be a native regulatory protein, i.e., one or more additional copies of the coding sequence for a regulatory protein that is naturally present in the cell. Alternatively, a regulatory protein can be heterologous to the cell, e.g., a transgenic Populus plant can contain the coding sequence for a transcription factor polypeptide from an Arabidopsis plant.

A regulatory protein can include additional amino acids that are not involved in modulating gene expression, and thus can be longer than would otherwise be the case. For example, a regulatory protein can include an amino acid sequence that functions as a reporter. Such a regulatory protein can be a fusion protein in which a green fluorescent protein (GFP) polypeptide is fused to, e.g., SEQ ID NO:865, or in which a yellow fluorescent protein (YFP) polypeptide is fused to, e.g., SEQ ID NO:1785. In some embodiments, a regulatory protein includes a purification tag, a chloroplast transit peptide, a mitochondrial transit peptide, or a leader sequence added to the amino or carboxyl terminus.

Regulatory protein candidates suitable for use in the invention can be identified by analysis of nucleotide and polypeptide sequence alignments. For example, performing a query on a database of nucleotide or polypeptide sequences can identify homologs and/or orthologs of regulatory proteins. Sequence analysis can involve BLAST, Reciprocal BLAST, or PSI-BLAST analysis of nonredundant databases using known regulatory protein amino acid sequences. Those polypeptides in the database that have greater than 40% sequence identity can be identified as candidates for further evaluation for suitability as regulatory proteins. Amino acid sequence similarity allows for conservative amino acid substitutions, such as substitution of one hydrophobic residue for another or substitution of one polar residue for another. If desired, manual inspection of such candidates can be carried out in order to narrow the number of candidates to be further evaluated. Manual inspection can be performed by selecting those candidates that appear to have domains suspected of being present in regulatory proteins, e.g., conserved functional domains.

The identification of conserved regions in a template or subject polypeptide can facilitate production of variants of regulatory proteins. Conserved regions can be identified by locating a region within the primary amino acid sequence of a template polypeptide that is a repeated sequence, forms some secondary structure (e.g., helices and beta sheets), establishes positively or negatively charged domains, or represents a protein motif or domain. See, e.g., the Pfam web site describing consensus sequences for a variety of protein motifs and domains at sanger.ac.uk/Pfam and genome.wustl.edu/Pfam. A description of the information included at the Pfam database is described in Sonnhammer et al., Nucl. Acids Res., 26:320-322 (1998); Sonnhammer et al., Proteins, 28:405-420 (1997); and Bateman et al., Nucl. Acids Res., 27:260-262 (1999). Amino acid residues corresponding to Pfam domains included in regulatory proteins provided herein are set forth in the Sequence Listing. For example, amino acid residues 115 to 179 of the amino acid sequence set forth in SEQ ID NO:304 correspond to a DHHC zinc finger domain, as indicated in fields <222> and <223> for SEQ ID NO:304 in the Sequence Listing.

Conserved regions also can be determined by aligning sequences of the same or related polypeptides from closely related species. Closely related species preferably are from the same family. In some embodiments, alignment of sequences from two different species is adequate. For example, sequences from Arabidopsis thaliana and Glycine max can be used to identify one or more conserved regions.

Typically, polypeptides that exhibit at least about 40% amino acid sequence identity are useful to identify conserved regions. Conserved regions of related polypeptides can exhibit at least 45% amino acid sequence identity, e.g., at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% amino acid sequence identity. In some embodiments, a conserved region of target and template polypeptides exhibit at least 92%, 94%, 96%, 98%, or 99% amino acid sequence identity. Amino acid sequence identity can be deduced from amino acid or nucleotide sequences. In certain cases, highly conserved domains have been identified within regulatory proteins. These conserved regions can be useful in identifying functionally similar (orthologous) regulatory proteins.

In some instances, suitable regulatory proteins can be synthesized on the basis of consensus functional domains and/or conserved regions in polypeptides that are homologous regulatory proteins. Domains are groups of substantially contiguous amino acids in a polypeptide that can be used to characterize protein families and/or parts of proteins. Such domains have a “fingerprint” or “signature” that can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three-dimensional conformation. Generally, domains are correlated with specific in vitro and/or in vivo activities. A domain can have a length of from 10 amino acids to 400 amino acids, e.g., 10 to 50 amino acids, or 25 to 100 amino acids, or 35 to 65 amino acids, or 35 to 55 amino acids, or 45 to 60 amino acids, or 200 to 300 amino acids, or 300 to 400 amino acids.

Representative homologs and/or orthologs of regulatory proteins are shown in FIGS. 1-51 and FIGS. 53-131. Each Figure represents an alignment of the amino acid sequence of a regulatory protein with the amino acid sequences of corresponding homologs and/or orthologs. Amino acid sequences of regulatory proteins and their corresponding homologs and/or orthologs have been aligned to identify conserved amino acids and to determine consensus sequences that contain frequently occurring amino acid residues at particular positions in the aligned sequences, as shown in FIGS. 1-51 and FIGS. 53-131. A dash in an aligned sequence represents a gap, i.e., a lack of an amino acid at that position. Identical amino acids or conserved amino acid substitutions among aligned sequences are identified by boxes.

Each consensus sequence is comprised of conserved regions. Each conserved region contains a sequence of contiguous amino acid residues. A dash in a consensus sequence indicates that the consensus sequence either lacks an amino acid at that position or includes an amino acid at that position. If an amino acid is present, the residue at that position corresponds to one found in any aligned sequence at that position.

Useful polypeptides can be constructed based on the consensus sequence in any of FIGS. 1-51 or FIGS. 53-131. Such a polypeptide includes the conserved regions in the selected consensus sequence, arranged in the order depicted in the Figure from amino-terminal end to carboxy-terminal end. Such a polypeptide may also include zero, one, or more than one amino acid in positions marked by dashes. When no amino acids are present at positions marked by dashes, the length of such a polypeptide is the sum of the amino acid residues in all conserved regions. When amino acids are present at all positions marked by dashes, such a polypeptide has a length that is the sum of the amino acid residues in all conserved regions and all dashes.

A conserved domain in certain cases may be 1) a localization domain, 2) an activation domain, 3) a repression domain, 4) an oligomerization domain or 5) a DNA binding domain. Consensus domains and conserved regions can be identified by homologous polypeptide sequence analysis as described above. The suitability of polypeptides for use as regulatory proteins can be evaluated by functional complementation studies.

A regulatory protein also can be a fragment of a naturally occurring regulatory protein. In certain cases, such as transcription factor regulatory proteins, a fragment can comprise the DNA-binding and transcription-regulating domains of the naturally occurring regulatory protein. Additional information on regulatory protein domains is provided below.

DNA Binding Domain

A regulatory protein can include a domain, termed a DNA binding domain, which binds to a recognized site on DNA. A DNA binding domain of a regulatory protein can bind to one or more specific cis-responsive promoter motifs described herein. The typical result is modulation of transcription from a transcriptional start site associated with and operably linked to the cis-responsive motif. In some embodiments, binding of a DNA binding domain to a cis-responsive motif in planta involves other cellular components, which can be supplied by the plant.

Transactivation Domain

A regulatory protein can have discrete DNA binding and transactivation domains. Typically, transactivation domains bring proteins of the cellular transcription and translation machinery into contact with the transcription start site to initiate transcription. A transactivation domain of a regulatory protein can be synthetic or can be naturally-occurring. An example of a transactivation domain is the transactivation domain of a maize transcription factor C polypeptide.

Oligomerization Sequences

In some embodiments, a regulatory protein comprises oligomerization sequences. In some instances oligomerization is required for a ligand/regulatory protein complex or protein/protein complex to bind to a recognized DNA site. Oligomerization sequences can permit a regulatory protein to produce either homo- or heterodimers. Several motifs or domains in the amino acid sequence of a regulatory protein can influence heterodimerization or homodimerization of a given regulatory protein.

In some embodiments, transgenic plants also include a recombinant coactivator polypeptide that can interact with a regulatory protein to mediate the regulatory protein's effect on transcription of an endogenous gene. Such polypeptides include chaperonins. In some embodiments, a recombinant coactivator polypeptide is a chimera of a non-plant coactivator polypeptide and a plant coactivator polypeptide. Thus, in some embodiments, a regulatory protein described herein binds as a heterodimer to a promoter motif. In such embodiments, plants and plant cells contain a coding sequence for a second or other regulatory protein as a dimerization or multimerization partner, in addition to the coding sequence for the first regulatory protein.

The identification of conserved regions in a regulatory protein facilitates production of variants of regulatory proteins. Variants of regulatory proteins typically have 10 or fewer conservative amino acid substitutions within the primary amino acid sequence, e.g., 7 or fewer conservative amino acid substitutions, 5 or fewer conservative amino acid substitutions, or between 1 and 5 conservative substitutions. A useful variant polypeptide can be constructed based on one of the alignments set forth in any one of FIGS. 1-51 and 53-131. Such a polypeptide includes the conserved regions, arranged in the order depicted in the Figure from amino-terminal end to carboxy-terminal end. Such a polypeptide may also include zero, one, or more than one amino acid in positions marked by dashes. When no amino acids are present at positions marked by dashes, the length of such a polypeptide is the sum of the amino acid residues in all conserved regions. When amino acids are present at all positions marked by dashes, such a polypeptide has a length that is the sum of the amino acid residues in all conserved regions and all dashes.

In some embodiments, useful regulatory proteins include those that fit a Hidden Markov Model based on the polypeptides set forth in any one of FIG. 1-51 or 53-131. A Hidden Markov Model (HMM) is a statistical model of a consensus sequence for a group of functional homologs. See, Durbin et al., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, UK (1998). An HMM is generated by the program HMMER 2.3.2 with default program parameters, using the sequences of the group of functional homologs as input. The multiple sequence alignment is generated by ProbCons (Do et al., Genome Res., 15(2):330-40 (2005)) version 1.11 using a set of default parameters: -c, --consistency REPS of 2; -ir, --iterative-refinement REPS of 100; -pre, --pre-training REPS of 0. ProbCons is a public domain software program provided by Stanford University. The alignments provided in the figures were generated using the program MUSCLE version 3.52 based on alignments generated by ProbCons.

The default parameters for building an HMM (hmmbuild) are as follows: the default “architecture prior” (archpri) used by MAP architecture construction is 0.85, and the default cutoff threshold (idlevel) used to determine the effective sequence number is 0.62. HMMER 2.3.2 was released Oct. 3, 2003 under a GNU general public license, and is available from various sources on the World Wide Web such as hmmer.janelia.org; hmmer.wustl.edu; and fr.com/hmmer232/. Hmmbuild outputs the model as a text file.

The HMM for a group of functional homologs can be used to determine the likelihood that a candidate regulatory protein sequence is a better fit to that particular HMM than to a null HMM generated using a group of sequences that are not structurally or functionally related. The likelihood that a candidate polypeptide sequence is a better fit to an HMM than to a null HMM is indicated by the HMM bit score, a number generated when the candidate sequence is fitted to the HMM profile using the HMMER hmmsearch program. The following default parameters are used when running hmmsearch: the default E-value cutoff (E) is 10.0, the default bit score cutoff (T) is negative infinity, the default number of sequences in a database (Z) is the real number of sequences in the database, the default E-value cutoff for the per-domain ranked hit list (domE) is infinity, and the default bit score cutoff for the per-domain ranked hit list (domT) is negative infinity. A high HMM bit score indicates a greater likelihood that the candidate sequence carries out one or more of the biochemical or physiological function(s) of the polypeptides used to generate the HMM. A high HMM bit score is at least about 20, and often is higher. Slight variations in the HMM bit score of a particular sequence can occur due to factors such as the order in which sequences are processed for alignment by multiple sequence alignment algorithms such as the ProbCons program. Nevertheless, such HMM bit score variation is minor.

The regulatory proteins discussed herein fit the indicated HMM with an HMM bit score greater than about 20 (e.g., greater than 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, or 500). In some embodiments, the HMM bit score of a regulatory protein discussed herein is about 50%, 60%, 70%, 80%, 90%, or 95% of the HMM bit score of a functional homolog provided in the Sequence Listing. In some embodiments, a regulatory protein discussed herein fits the indicated HMM with an HMM bit score greater than about 20, and has a domain indicative of a regulatory protein. In some embodiments, a regulatory protein discussed herein fits the indicated HMM with an HMM bit score greater than about 20, and has 30% or greater sequence identity (e.g., 75%, 80%, 85%, 90%, 95%, or 100% sequence identity) to an amino acid sequence shown in any one of FIG. 1-51 or 53-131.

Polypeptides are shown in the Sequence Listing that have HMM bit scores greater than about 25 when fitted to an HMM generated from the amino acid sequences set forth in FIG. 28. Such polypeptides include Ceres CLONE ID no. 1940689 (SEQ ID NO:581), Public GI no. 34907702 (SEQ ID NO:575), Ceres CLONE ID no. 324760 (SEQ ID NO:579), Ceres CLONE ID no. 474693 (SEQ ID NO:576), Ceres CLONE ID no. 1806146 (SEQ ID NO:2063), Ceres ANNOT ID no. 1525350 (SEQ ID NO:570), Ceres ANNOT ID no. 1445304 (SEQ ID NO:578), Public GI no. 6850309 (SEQ ID NO:568), Ceres ANNOT ID no. 1498288 (SEQ ID NO:572), Ceres CLONE ID no. 21406 (SEQ ID NO:566), Public GI no. 24030386 (SEQ ID NO:567), and Ceres ANNOT ID no. 1471938 (SEQ ID NO:574).

Polypeptides are shown in the Sequence Listing that have HMM bit scores greater than about 55 when fitted to an HMM generated from the amino acid sequences set forth in FIG. 30. Such polypeptides include Ceres ANNOT ID no. 6042920 (SEQ ID NO:2276), Ceres CLONE ID no. 690625 (SEQ ID NO:594), Ceres CLONE ID no. 22671 (SEQ ID NO:590), Ceres ANNOT ID no. 1467420 (SEQ ID NO:596), Ceres ANNOT ID no. 1483277 (SEQ ID NO:593), Ceres CLONE ID no. 1079601 (SEQ ID NO:591), and Public GI no. 15042132 (SEQ ID NO:597).

Polypeptides are shown in the Sequence Listing that have HMM bit scores greater than about 230 when fitted to an HMM generated from the amino acid sequences set forth in FIG. 53. Such polypeptides include Ceres ANNOT ID no. 1533351 (SEQ ID NO:849), Ceres ANNOT ID no. 1480628 (SEQ ID NO:843), Ceres CLONE ID no. 158765 (SEQ ID NO:839), Public GI no. 5669656 (SEQ ID NO:844), Ceres ANNOT ID no. 6064763 (SEQ ID NO:2296), Ceres CLONE ID no. 3900 (SEQ ID NO:838), Ceres CLONE ID no. 282892 (SEQ ID NO:850), Ceres CLONE ID no. 1322549 (SEQ ID NO:847), Ceres CLONE ID no. 1329861 (SEQ ID NO:845), Ceres CLONE ID no. 1839717 (SEQ ID NO:841), and Ceres CLONE ID no. 537752 (SEQ ID NO:846).

Polypeptides are shown in the Sequence Listing that have HMM bit scores greater than about 210 when fitted to an HMM generated from the amino acid sequences set forth in FIG. 75. Such polypeptides include Ceres ANNOT ID no. 1521997 (SEQ ID NO:1254), Ceres CLONE ID no. 272426 (SEQ ID NO:2017), Ceres CLONE ID no. 245683 (SEQ ID NO:2015), Ceres CLONE ID no. 1283552 (SEQ ID NO:2016), Ceres ANNOT ID no. 1468633 (SEQ ID NO:1255), Ceres ANNOT ID no. 1473854 (SEQ ID NO:1251), Ceres CLONE ID no. 659723 (SEQ ID NO:2012), Ceres CLONE ID no. 824827 (SEQ ID NO:2018), Ceres CLONE ID no. 1784110 (SEQ ID NO:1257), Ceres CLONE ID no. 1585988 (SEQ ID NO:2014), Ceres CLONE ID no. 21604 (SEQ ID NO:1249), and Ceres CLONE ID no. 953644 (SEQ ID NO:2013).

Polypeptides are shown in the Sequence Listing that have HMM bit scores greater than about 230 when fitted to an HMM generated from the amino acid sequences set forth in FIG. 81. Such polypeptides include Ceres ANNOT ID no. 1451585 (SEQ ID NO:1327), Ceres CLONE ID no. 1886324 (SEQ ID NO:1331), Public GI No. 1429228 (SEQ ID NO:1945), Public GI No. 57899877 (SEQ ID NO:1942), Ceres ANNOT ID no. 1504670 (SEQ ID NO:1325), Ceres CLONE ID no. 1541168 (SEQ ID NO:1939), Public GI No. 55585039 (SEQ ID NO:1941), Ceres CLONE ID no. 1785734 (SEQ ID NO:1329), Ceres CLONE ID no. 530235 (SEQ ID NO:1943), Ceres CLONE ID no. 225321 (SEQ ID NO:1323), Ceres CLONE ID no. 8364 (SEQ ID NO:1944), and Ceres CLONE ID no. 699465 (SEQ ID NO:1940).

Polypeptides are shown in the Sequence Listing that have HMM bit scores greater than about 145 when fitted to an HMM generated from the amino acid sequences set forth in FIG. 107. Such polypeptides include Ceres ANNOT ID no. 1533409 (SEQ ID NO:1593), Public GI no. 37991859 (SEQ ID NO:2055), Ceres CLONE ID no. 1958407 (SEQ ID NO:2157), Ceres CLONE ID no. 327449 (SEQ ID NO:2054), Ceres ANNOT ID no. 1484716 (SEQ ID NO:1587), Ceres ANNOT ID no. 1499354 (SEQ ID NO:1589), Ceres ANNOT ID no. 1491719 (SEQ ID NO:1591), Ceres CLONE ID no. 397320 (SEQ ID NO:1585), Ceres CLONE ID no. 1066463 (SEQ ID NO:2052), Ceres CLONE ID no. 476445 (SEQ ID NO:2053), Ceres CLONE ID no. 19640 (SEQ ID NO:2049), Public GI no. 19310623 (SEQ ID NO:2050), Ceres CLONE ID no. 1099781 (SEQ ID NO:2051), Public GI no. 8778455 (SEQ ID NO:2048), Ceres CLONE ID no. 1349 (SEQ ID NO:2046), and Public GI no. 62318582 (SEQ ID NO:2047).

Polypeptides are shown in the Sequence Listing that have HMM bit scores greater than about 355 when fitted to an HMM generated from the amino acid sequences set forth in FIG. 119. Such polypeptides include Ceres Annot ID no. 552542 (SEQ ID NO:1722), Ceres ANNOT ID no. 1460742 (SEQ ID NO:1726), Ceres ANNOT ID no. 1514007 (SEQ ID NO:1724), Ceres CLONE ID no. 1548279 (SEQ ID NO:1995), Ceres CLONE ID no. 1044645 (SEQ ID NO:1994), Ceres CLONE ID no. 727056 (SEQ ID NO:1996), and Public GI no. 52077327 (SEQ ID NO:1993).

Nucleic Acids Encoding Regulatory Proteins

Nucleic acids encoding regulatory proteins are described herein. Such nucleic acid can comprise a coding sequence that encodes any of the regulatory proteins as set forth in SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, SEQ ID NO:2087, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, or SEQ ID NO:2348.

Examples of nucleic acids encoding regulatory proteins are set forth in SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:118, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:129, SEQ ID NO:133, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:148, SEQ ID NO:150, SEQ ID NO:156, SEQ ID NO:158, SEQ ID NO:160, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:169, SEQ ID NO:171, SEQ ID NO:177, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:271, SEQ ID NO:274, SEQ ID NO:278, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:314, SEQ ID NO:317, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:327, SEQ ID NO:329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:336, SEQ ID NO:338, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:352, SEQ ID NO:354, SEQ ID NO:356, SEQ ID NO:360, SEQ ID NO:369, SEQ ID NO:371, SEQ ID NO:373, SEQ ID NO:376, SEQ ID NO:378, SEQ ID NO:380, SEQ ID NO:386, SEQ ID NO:390, SEQ ID NO:393, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID NO:416, SEQ ID NO:431, SEQ ID NO:435, SEQ ID NO:437, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:444, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:453, SEQ ID NO:458, SEQ ID NO:460, SEQ ID NO:464, SEQ ID NO:469, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:477, SEQ ID NO:482, SEQ ID NO:486, SEQ ID NO:489, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:500, SEQ ID NO:503, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:515, SEQ ID NO:517, SEQ ID NO:519, SEQ ID NO:523, SEQ ID NO:525, SEQ ID NO:528, SEQ ID NO:534, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:544, SEQ ID NO:547, SEQ ID NO:552, SEQ ID NO:554, SEQ ID NO:562, SEQ ID NO:565, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:573, SEQ ID NO:577, SEQ ID NO:580, SEQ ID NO:582, SEQ ID NO:584, SEQ ID NO:589, SEQ ID NO:592, SEQ ID NO:595, SEQ ID NO:598, SEQ ID NO:600, SEQ ID NO:602, SEQ ID NO:605, SEQ ID NO:607, SEQ ID NO:609, SEQ ID NO:611, SEQ ID NO:613, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:637, SEQ ID NO:649, SEQ ID NO:651, SEQ ID NO:655, SEQ ID NO:658, SEQ ID NO:660, SEQ ID NO:664, SEQ ID NO:670, SEQ ID NO:674, SEQ ID NO:677, SEQ ID NO:679, SEQ ID NO:681, SEQ ID NO:683, SEQ ID NO:685, SEQ ID NO:688, SEQ ID NO:694, SEQ ID NO:697, SEQ ID NO:699, SEQ ID NO:702, SEQ ID NO:704, SEQ ID NO:706, SEQ ID NO:708, SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:717, SEQ ID NO:719, SEQ ID NO:721, SEQ ID NO:723, SEQ ID NO:729, SEQ ID NO:736, SEQ ID NO:741, SEQ ID NO:743, SEQ ID NO:746, SEQ ID NO:752, SEQ ID NO:754, SEQ ID NO:759, SEQ ID NO:764, SEQ ID NO:778, SEQ ID NO:780, SEQ ID NO:785, SEQ ID NO:789, SEQ ID NO:792, SEQ ID NO:795, SEQ ID NO:797, SEQ ID NO:799, SEQ ID NO:801, SEQ ID NO:807, SEQ ID NO:810, SEQ ID NO:813, SEQ ID NO:815, SEQ ID NO:819, SEQ ID NO:821, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:829, SEQ ID NO:832, SEQ ID NO:834, SEQ ID NO:837, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:848, SEQ ID NO:851, SEQ ID NO:854, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:864, SEQ ID NO:867, SEQ ID NO:884, SEQ ID NO:889, SEQ ID NO:891, SEQ ID NO:893, SEQ ID NO:895, SEQ ID NO:897, SEQ ID NO:899, SEQ ID NO:903, SEQ ID NO:906, SEQ ID NO:911, SEQ ID NO:913, SEQ ID NO:916, SEQ ID NO:918, SEQ ID NO:920, SEQ ID NO:926, SEQ ID NO:928, SEQ ID NO:933, SEQ ID NO:935, SEQ ID NO:937, SEQ ID NO:942, SEQ ID NO:944, SEQ ID NO:958, SEQ ID NO:963, SEQ ID NO:965, SEQ ID NO:967, SEQ ID NO:972, SEQ ID NO:974, SEQ ID NO:979, SEQ ID NO:981, SEQ ID NO:993, SEQ ID NO:1006, SEQ ID NO:1010, SEQ ID NO:1015, SEQ ID NO:1027, SEQ ID NO:1030, SEQ ID NO:1034, SEQ ID NO:1049, SEQ ID NO:1051, SEQ ID NO:1054, SEQ ID NO:1057, SEQ ID NO:1059, SEQ ID NO:1061, SEQ ID NO:1063, SEQ ID NO:1067, SEQ ID NO:1070, SEQ ID NO:1077, SEQ ID NO:1080, SEQ ID NO:1082, SEQ ID NO:1084, SEQ ID NO:1086, SEQ ID NO:1090, SEQ ID NO:1093, SEQ ID NO:1095, SEQ ID NO:1097, SEQ ID NO:1103, SEQ ID NO:1108, SEQ ID NO:1116, SEQ ID NO:1121, SEQ ID NO:1124, SEQ ID NO:1128, SEQ ID NO:1130, SEQ ID NO:1133, SEQ ID NO:1135, SEQ ID NO:1138, SEQ ID NO:1142, SEQ ID NO:1148, SEQ ID NO:1155, SEQ ID NO:1158, SEQ ID NO:1160, SEQ ID NO:1162, SEQ ID NO:1164, SEQ ID NO:1170, SEQ ID NO:1172, SEQ ID NO:1175, SEQ ID NO:1182, SEQ ID NO:1184, SEQ ID NO:1208, SEQ ID NO:1210, SEQ ID NO:1212, SEQ ID NO:1214, SEQ ID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1236, SEQ ID NO:1238, SEQ ID NO:1240, SEQ ID NO:1242, SEQ ID NO:1244, SEQ ID NO:1246, SEQ ID NO:1248, SEQ ID NO:1250, SEQ ID NO:1252, SEQ ID NO:1254, SEQ ID NO:1256, SEQ ID NO:1258, SEQ ID NO:1260, SEQ ID NO:1262, SEQ ID NO:1264, SEQ ID NO:1266, SEQ ID NO:1268, SEQ ID NO:1270, SEQ ID NO:1272, SEQ ID NO:1274, SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1282, SEQ ID NO:1284, SEQ ID NO:1291, SEQ ID NO:1293, SEQ ID NO:1295, SEQ ID NO:1297, SEQ ID NO:1299, SEQ ID NO:1301, SEQ ID NO:1310, SEQ ID NO:1312, SEQ ID NO:1314, SEQ ID NO:1316, SEQ ID NO:1318, SEQ ID NO:1320, SEQ ID NO:1322, SEQ ID NO:1324, SEQ ID NO:1326, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1332, SEQ ID NO:1334, SEQ ID NO:1336, SEQ ID NO:1338, SEQ ID NO:1340, SEQ ID NO:1342, SEQ ID NO:1344, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1356, SEQ ID NO:1358, SEQ ID NO:1360, SEQ ID NO:1368, SEQ ID NO:1370, SEQ ID NO:1372, SEQ ID NO:1374, SEQ ID NO:1376, SEQ ID NO:1378, SEQ ID NO:1380, SEQ ID NO:1382, SEQ ID NO:1384, SEQ ID NO:1386, SEQ ID NO:1388, SEQ ID NO:1390, SEQ ID NO:1392, SEQ ID NO:1394, SEQ ID NO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1402, SEQ ID NO:1404, SEQ ID NO:1411, SEQ ID NO:1413, SEQ ID NO:1416, SEQ ID NO:1418, SEQ ID NO:1420, SEQ ID NO:1422, SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1434, SEQ ID NO:1435, SEQ ID NO:1443, SEQ ID NO:1464, SEQ ID NO:1466, SEQ ID NO:1468, SEQ ID NO:1470, SEQ ID NO:1472, SEQ ID NO:1474, SEQ ID NO:1476, SEQ ID NO:1478, SEQ ID NO:1480, SEQ ID NO:1482, SEQ ID NO:1484, SEQ ID NO:1486, SEQ ID NO:1492, SEQ ID NO:1501, SEQ ID NO:1503, SEQ ID NO:1517, SEQ ID NO:1519, SEQ ID NO:1521, SEQ ID NO:1523, SEQ ID NO:1525, SEQ ID NO:1527, SEQ ID NO:1535, SEQ ID NO:1537, SEQ ID NO:1539, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1549, SEQ ID NO:1551, SEQ ID NO:1553, SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1563, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID SEQ ID NO:1569, SEQ ID NO:1572, SEQ ID NO:1574, SEQ ID NO:1576, SEQ ID NO:1578, SEQ ID NO:1580, SEQ ID NO:1582, SEQ ID NO:1584, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1594, SEQ ID NO:1609, SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1619, SEQ ID NO:1623, SEQ ID NO:1625, SEQ ID NO:1627, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1636, SEQ ID NO:1652, SEQ ID NO:1656, SEQ ID NO:1658, SEQ ID NO:1660, SEQ ID NO:1662, SEQ ID NO:1664, SEQ ID NO:1666, SEQ ID NO:1668, SEQ ID NO:1670, SEQ ID NO:1672, SEQ ID NO:1674, SEQ ID NO:1680, SEQ ID NO:1682, SEQ ID NO:1691, SEQ ID NO:1693, SEQ ID NO:1695, SEQ ID NO:1697, SEQ ID NO:1699, SEQ ID NO:1701, SEQ ID NO:1703, SEQ ID NO:1705, SEQ ID NO:1707, SEQ ID NO:1709, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1715, SEQ ID NO:1717, SEQ ID NO:1719, SEQ ID NO:1721, SEQ ID NO:1723, SEQ ID NO:1725, SEQ ID NO:1727, SEQ ID NO:1732, SEQ ID NO:1734, SEQ ID NO:1748, SEQ ID NO:1751, SEQ ID NO:1766, SEQ ID NO:1776, SEQ ID NO:1778, SEQ ID NO:1780, SEQ ID NO:1782, SEQ ID NO:1784, SEQ ID NO:1805, SEQ ID NO:1821, SEQ ID NO:1823, SEQ ID NO:1825, SEQ ID NO:1827, SEQ ID NO:1829, SEQ ID NO:1831, SEQ ID NO:1833, SEQ ID NO:1835, SEQ ID NO:1837, SEQ ID NO:1839, SEQ ID NO:1841, SEQ ID NO:1843, SEQ ID NO:1845, SEQ ID NO:1847, SEQ ID NO:1849, SEQ ID NO:1851, SEQ ID NO:1853, SEQ ID NO:1855, SEQ ID NO:1857, SEQ ID NO:1859, SEQ ID NO:1861, SEQ ID NO:1863, SEQ ID NO:1865, SEQ ID NO:1867, SEQ ID NO:1869, SEQ ID NO:1871, SEQ ID NO:1873, SEQ ID NO:1875, SEQ ID NO:1877, SEQ ID NO:1879, SEQ ID NO:1881, SEQ ID NO:1883, SEQ ID NO:1885, SEQ ID NO:1887, SEQ ID NO:1889, SEQ ID NO:1891, SEQ ID NO:1896, SEQ ID NO:1898, SEQ ID NO:1900, SEQ ID NO:1903, SEQ ID NO:1905, SEQ ID NO:1907, SEQ ID NO:1919, SEQ ID NO:1920, SEQ ID NO:2060, SEQ ID NO:2062, SEQ ID NO:2064, SEQ ID NO:2084, SEQ ID NO:2088, SEQ ID NO:2090, SEQ ID NO:2092, SEQ ID NO:2094, SEQ ID NO:2096, SEQ ID NO:2098, SEQ ID NO:2100, SEQ ID NO:2102, SEQ ID NO:2104, SEQ ID NO:2106, SEQ ID NO:2108, SEQ ID NO:2110, SEQ ID NO:2112, SEQ ID NO:2114, SEQ ID NO:2116, SEQ ID NO:2118, SEQ ID NO:2120, SEQ ID NO:2122, SEQ ID NO:2124, SEQ ID NO:2126, SEQ ID NO:2128, SEQ ID NO:2130, SEQ ID NO:2132, SEQ ID NO:2134, SEQ ID NO:2136, SEQ ID NO:2138, SEQ ID NO:2140, SEQ ID NO:2142, SEQ ID NO:2144, SEQ ID NO:2146, SEQ ID NO:2148, SEQ ID NO:2150, SEQ ID NO:2152, SEQ ID NO:2154, SEQ ID NO:2156, SEQ ID NO:2158, SEQ ID NO:2160, SEQ ID NO:2161, SEQ ID NO:2163, SEQ ID NO:2165, SEQ ID NO:6167, SEQ ID NO:2169, SEQ ID NO:2171, SEQ ID NO:2173, SEQ ID NO:2175, SEQ ID NO:2177, SEQ ID NO:2179, SEQ ID NO:2181, SEQ ID NO:2183, SEQ ID NO:2185, SEQ ID NO:2187, SEQ ID NO:2189, SEQ ID NO:2191, SEQ ID NO:2193, SEQ ID NO:2195, SEQ ID NO:2197, SEQ ID NO:2199, SEQ ID NO:2201, SEQ ID NO:2203, SEQ ID NO:2205, SEQ ID NO:2207, SEQ ID NO:2209, SEQ ID NO:2211, SEQ ID NO:2213, SEQ ID NO:2215, SEQ ID NO:2217, SEQ ID NO:2219, SEQ ID NO:2221, SEQ ID NO:2223, SEQ ID NO:2225, SEQ ID NO:2227, SEQ ID NO:2229, SEQ ID NO:2231, SEQ ID NO:2233, SEQ ID NO:2235, SEQ ID NO:2237, SEQ ID NO:2239, SEQ ID NO:2241, SEQ ID NO:2243, SEQ ID NO:2245, SEQ ID NO:2247, SEQ ID NO:2249, SEQ ID NO:2251, SEQ ID NO:2253, SEQ ID NO:2255, SEQ ID NO:2257, SEQ ID NO:2259, SEQ ID NO:2261, SEQ ID NO:2263, SEQ ID NO:2265, SEQ ID NO:2267, SEQ ID NO:2269, SEQ ID NO:2271, SEQ ID NO:2273, SEQ ID NO:2275, SEQ ID NO:2277, SEQ ID NO:2279, SEQ ID NO:2281, SEQ ID NO:2283, SEQ ID NO:2285, SEQ ID NO:2287, SEQ ID NO:2289, SEQ ID NO:2291, SEQ ID NO:2293, SEQ ID NO:2295, SEQ ID NO:2297, SEQ ID NO:2299, SEQ ID NO:2301, SEQ ID NO:2303, SEQ ID NO:2305, SEQ ID NO:2307, SEQ ID NO:2309, SEQ ID NO:2311, SEQ ID NO:2313, SEQ ID NO:2315, SEQ ID NO:2317, SEQ ID NO:2319, SEQ ID NO:2321, SEQ ID NO:2323, SEQ ID NO:2325, SEQ ID NO:2327, SEQ ID NO:2329, SEQ ID NO:2331, SEQ ID NO:2333, SEQ ID NO:2335, SEQ ID NO:2337, SEQ ID NO:2339, SEQ ID NO:2341, SEQ ID NO:2343, SEQ ID NO:2345, SEQ ID NO:2347, and SEQ ID NO:2349-2690.

SEQ ID NO:97, SEQ ID NO:101, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:129, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:150, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:271, SEQ ID NO:274, SEQ ID NO:278, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:314, SEQ ID NO:317, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:327, SEQ ID NO:329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:352, SEQ ID NO:376, SEQ ID NO:386, SEQ ID NO:390, SEQ ID NO:393, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:453, SEQ ID NO:458, SEQ ID NO:469, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:477, SEQ ID NO:482, SEQ ID NO:486, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:500, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:515, SEQ ID NO:534, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:544, SEQ ID NO:552, SEQ ID NO:562, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:573, SEQ ID NO:577, SEQ ID NO:580, SEQ ID NO:592, SEQ ID NO:595, SEQ ID NO:602, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:649, SEQ ID NO:655, SEQ ID NO:658, SEQ ID NO:664, SEQ ID NO:674, SEQ ID NO:681, SEQ ID NO:683, SEQ ID NO:699, SEQ ID NO:704, SEQ ID NO:708, SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:717, SEQ ID NO:719, SEQ ID NO:721, SEQ ID NO:723, SEQ ID NO:741, and SEQ ID NO:746 are predicted to encode polypeptides having the amino acid sequences set forth in SEQ ID NO:98, SEQ ID NO:102, SEQ ID NO:108, SEQ ID NO:110, SEQ ID NO:114, SEQ ID NO:124, SEQ ID NO:126, SEQ ID NO:130, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NO:145, SEQ ID NO:151, SEQ ID NO:196, SEQ ID NO:198, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NO:253, SEQ ID NO:255, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NO:262, SEQ ID NO:267, SEQ ID NO:269, SEQ ID NO:272, SEQ ID NO:275, SEQ ID NO:279, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NO:286, SEQ ID NO:289, SEQ ID NO:292, SEQ ID NO:294, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NO:308, SEQ ID NO:315, SEQ ID NO:318, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NO:325, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NO:334, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347, SEQ ID NO:353, SEQ ID NO:377, SEQ ID NO:387, SEQ ID NO:391, SEQ ID NO:394, SEQ ID NO:400, SEQ ID NO:402, SEQ ID NO:440, SEQ ID NO:442, SEQ ID NO:449, SEQ ID NO:451, SEQ ID NO:454, SEQ ID NO:459, SEQ ID NO:470, SEQ ID NO:473, SEQ ID NO:475, SEQ ID NO:478, SEQ ID NO:483, SEQ ID NO:487, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NO:496, SEQ ID NO:501, SEQ ID NO:508, SEQ ID NO:510, SEQ ID NO:516, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NO:545, SEQ ID NO:553, SEQ ID NO:563, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NO:574, SEQ ID NO:578, SEQ ID NO:581, SEQ ID NO:593, SEQ ID NO:596, SEQ ID NO:603, SEQ ID NO:619, SEQ ID NO:621, SEQ ID NO:650, SEQ ID NO:656, SEQ ID NO:659, SEQ ID NO:665, SEQ ID NO:675, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NO:700, SEQ ID NO:705, SEQ ID NO:709, SEQ ID NO:713, SEQ ID NO:715, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NO:724, and SEQ ID NO:747, respectively.

SEQ ID NO:752, SEQ ID NO:754, SEQ ID NO:764, SEQ ID NO:785, SEQ ID NO:789, SEQ ID NO:795, SEQ ID NO:797, SEQ ID NO:799, SEQ ID NO:801, SEQ ID NO:810, SEQ ID NO:819, SEQ ID NO:821, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:829, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:848, SEQ ID NO:854, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:867, SEQ ID NO:889, SEQ ID NO:891, SEQ ID NO:893, SEQ ID NO:895, SEQ ID NO:903, SEQ ID NO:906, SEQ ID NO:911, SEQ ID NO:916, SEQ ID NO:918, SEQ ID NO:920, SEQ ID NO:926, SEQ ID NO:928, SEQ ID NO:942, SEQ ID NO:944, SEQ ID NO:958, SEQ ID NO:965, SEQ ID NO:967, SEQ ID NO:972, SEQ ID NO:974, SEQ ID NO:981, SEQ ID NO:1006, SEQ ID NO:1010, SEQ ID NO:1015, SEQ ID NO:1027, SEQ ID NO:1030, SEQ ID NO:1034, SEQ ID NO:1054, SEQ ID NO:1067, SEQ ID NO:1070, SEQ ID NO:1077, SEQ ID NO:1084, SEQ ID NO:1086, SEQ ID NO:1090, SEQ ID NO:1093, SEQ ID NO:1097, SEQ ID NO:1108, SEQ ID NO:1116, SEQ ID NO:1121, SEQ ID NO:1124, SEQ ID NO:1138, SEQ ID NO:1142, SEQ ID NO:1148, SEQ ID NO:1155, SEQ ID NO:1158, SEQ ID NO:1160, SEQ ID NO:1170, SEQ ID NO:1172, SEQ ID NO:1175, SEQ ID NO:1208, SEQ ID NO:1212, SEQ ID NO:1214, SEQ ID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1236, SEQ ID NO:1240, SEQ ID NO:1242, SEQ ID NO:1244, SEQ ID NO:1246, SEQ ID NO:1250, SEQ ID NO:1252, SEQ ID NO:1254, SEQ ID NO:1256, SEQ ID NO:1260, SEQ ID NO:1262, SEQ ID NO:1264, SEQ ID NO:1268, SEQ ID NO:1270, SEQ ID NO:1272, SEQ ID NO:1274, SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1282, SEQ ID NO:1291, SEQ ID NO:1295, SEQ ID NO:1297, SEQ ID NO:1299, SEQ ID NO:1310, SEQ ID NO:1312, SEQ ID NO:1316, SEQ ID NO:1318, SEQ ID NO:1320, SEQ ID NO:1324, SEQ ID NO:1326, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1334, SEQ ID NO:1336, SEQ ID NO:1338 are predicted to encode polypeptides having the amino acid sequences set forth in SEQ ID NO:753, SEQ ID NO:755, SEQ ID NO:765, SEQ ID NO:786, SEQ ID NO:780, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NO:802, SEQ ID NO:811, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:830, SEQ ID NO:841, SEQ ID NO:843, SEQ ID NO:849, SEQ ID NO:855, SEQ ID NO:859, SEQ ID NO:861, SEQ ID NO:868, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:904, SEQ ID NO:907, SEQ ID NO:912, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NO:921, SEQ ID NO:927, SEQ ID NO:929, SEQ ID NO:943, SEQ ID NO:945, SEQ ID NO:959, SEQ ID NO:966, SEQ ID NO:968, SEQ ID NO:973, SEQ ID NO:975, SEQ ID NO:982, SEQ ID NO:1007, SEQ ID NO:1011, SEQ ID NO:1016, SEQ ID NO:1028, SEQ ID NO:1031, SEQ ID NO:1035, SEQ ID NO:1055, SEQ ID NO:1068, SEQ ID NO:1071, SEQ ID NO:1078, SEQ ID NO:1085, SEQ ID NO:1087, SEQ ID NO:1091, SEQ ID NO:1094, SEQ ID NO:1098, SEQ ID NO:1109, SEQ ID NO:1117, SEQ ID NO:1122, SEQ ID NO:1125, SEQ ID NO:1139, SEQ ID NO:1143, SEQ ID NO:1149, SEQ ID NO:1156, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1171, SEQ ID NO:1173, SEQ ID NO:1176, SEQ ID NO:1209, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NO:1225, SEQ ID NO:1237, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NO:1292, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1335, SEQ ID NO:1337, and SEQ ID NO:1339, respectively.

SEQ ID NO:1340, SEQ ID NO:1342, SEQ ID NO:1344, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1356, SEQ ID NO:1358, SEQ ID NO:1368, SEQ ID NO:1372, SEQ ID NO:1374, SEQ ID NO:1378, SEQ ID NO:1380, SEQ ID NO:1384, SEQ ID NO:1386, SEQ ID NO:1388, SEQ ID NO:1390, SEQ ID NO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1402, SEQ ID NO:1411, SEQ ID NO:1416, SEQ ID NO:1418, SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1466, SEQ ID NO:1470, SEQ ID NO:1476, SEQ ID NO:1478, SEQ ID NO:1482, SEQ ID NO:1484, SEQ ID NO:1486, SEQ ID NO:1501, SEQ ID NO:1519, SEQ ID NO:1521, SEQ ID NO:1523, SEQ ID NO:1527, SEQ ID NO:1535, SEQ ID NO:1537, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1549, SEQ ID NO:1553, SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID NO:1574, SEQ ID NO:1576, SEQ ID NO:1578, SEQ ID NO:1582, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1623, SEQ ID NO:1625, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1656, SEQ ID NO:1658, SEQ ID NO:1662, SEQ ID NO:1664, SEQ ID NO:1666, SEQ ID NO:1668, SEQ ID NO:1670, SEQ ID NO:1672, SEQ ID NO:1682, SEQ ID NO:1693, SEQ ID NO:1695, SEQ ID NO:1699, SEQ ID NO:1701, SEQ ID NO:1703, SEQ ID NO:1705, SEQ ID NO:1707, SEQ ID NO:1709, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1715, SEQ ID NO:1717, SEQ ID NO:1719, SEQ ID NO:1723, SEQ ID NO:1725, SEQ ID NO:1732, SEQ ID NO:1748, SEQ ID NO:1776, SEQ ID NO:1780, SEQ ID NO:1782, SEQ ID NO:1833, SEQ ID NO:1855, SEQ ID NO:1891, SEQ ID NO:1898, SEQ ID NO:1900, SEQ ID NO:1907, SEQ ID NO:2060, SEQ ID NO:2062, and SEQ ID NO:2064 are predicted to encode polypeptides having the amino acid sequences set forth in SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NO:1369, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NO:1412, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NO:1467, SEQ ID NO:1471, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NO:1487, SEQ ID NO:1502, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1528, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1583, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1630, SEQ ID NO:1632, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NO:1683, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710, SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NO:1733, SEQ ID NO:1749, SEQ ID NO:1777, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NO:1834, SEQ ID NO:1856, SEQ ID NO:1892, SEQ ID NO:1899, SEQ ID NO:1901, SEQ ID NO:1908, SEQ ID NO:2061, SEQ ID NO:2063, and SEQ ID NO:2065, respectively.

SEQ ID NO:2088, SEQ ID NO:2090, SEQ ID NO:2092, SEQ ID NO:2094, SEQ ID NO:2096, SEQ ID NO:2098, SEQ ID NO:2100, SEQ ID NO:2102, SEQ ID NO:2104, SEQ ID NO:2106, SEQ ID NO:2108, SEQ ID NO:2110, SEQ ID NO:2112, SEQ ID NO:2114, SEQ ID NO:2116, SEQ ID NO:2118, SEQ ID NO:2120, SEQ ID NO:2122, SEQ ID NO:2124, SEQ ID NO:2126, SEQ ID NO:2128, SEQ ID NO:2130, SEQ ID NO:2132, SEQ ID NO:2134, SEQ ID NO:2136, SEQ ID NO:2138, SEQ ID NO:2140, SEQ ID NO:2142, SEQ ID NO:2144, SEQ ID NO:2146, SEQ ID NO:2148, SEQ ID NO:2150, SEQ ID NO:2152, SEQ ID NO:2154, SEQ ID NO:2156, SEQ ID NO:2158, SEQ ID NO:2160, SEQ ID NO:2161, SEQ ID NO:2163, SEQ ID NO:2165, SEQ ID NO:6167, SEQ ID NO:2169, SEQ ID NO:2171, SEQ ID NO:2173, SEQ ID NO:2175, SEQ ID NO:2177, SEQ ID NO:2179, SEQ ID NO:2181, SEQ ID NO:2183, SEQ ID NO:2185, SEQ ID NO:2187, SEQ ID NO:2189, SEQ ID NO:2191, SEQ ID NO:2193, SEQ ID NO:2195, SEQ ID NO:2197, SEQ ID NO:2199, SEQ ID NO:2201, SEQ ID NO:2203, SEQ ID NO:2205, SEQ ID NO:2207, SEQ ID NO:2209, SEQ ID NO:2211, SEQ ID NO:2213, SEQ ID NO:2215, SEQ ID NO:2217, SEQ ID NO:2219, SEQ ID NO:2221, SEQ ID NO:2223, SEQ ID NO:2225, SEQ ID NO:2227, SEQ ID NO:2229, SEQ ID NO:2231, SEQ ID NO:2233, SEQ ID NO:2235, SEQ ID NO:2237, SEQ ID NO:2239, SEQ ID NO:2241, SEQ ID NO:2243, SEQ ID NO:2245, SEQ ID NO:2247, SEQ ID NO:2249, SEQ ID NO:2251, SEQ ID NO:2253, SEQ ID NO:2255, SEQ ID NO:2257, SEQ ID NO:2259, SEQ ID NO:2261, SEQ ID NO:2263, SEQ ID NO:2265, SEQ ID NO:2267, SEQ ID NO:2269, SEQ ID NO:2271, SEQ ID NO:2273, SEQ ID NO:2275, SEQ ID NO:2277, SEQ ID NO:2279, SEQ ID NO:2281, SEQ ID NO:2283, SEQ ID NO:2285, SEQ ID NO:2287, SEQ ID NO:2289, SEQ ID NO:2291, SEQ ID NO:2293, SEQ ID NO:2295, SEQ ID NO:2297, SEQ ID NO:2299, SEQ ID NO:2301, SEQ ID NO:2303, SEQ ID NO:2305, SEQ ID NO:2307, SEQ ID NO:2309, SEQ ID NO:2311, SEQ ID NO:2313, SEQ ID NO:2315, SEQ ID NO:2317, SEQ ID NO:2319, SEQ ID NO:2321, SEQ ID NO:2323, SEQ ID NO:2325, SEQ ID NO:2327, SEQ ID NO:2329, SEQ ID NO:2331, SEQ ID NO:2333, SEQ ID NO:2335, SEQ ID NO:2337, SEQ ID NO:2339, SEQ ID NO:2341, SEQ ID NO:2343, SEQ ID NO:2345, SEQ ID NO:2347, and SEQ ID NO:2690 are predicted to encode polypeptides having the amino acid sequences set forth in SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, SEQ ID NO:2348, and SEQ ID NO:1747, respectively.

In some cases, a recombinant nucleic acid construct can include a nucleic acid comprising less than the full-length coding sequence of a regulatory protein. A nucleic acid can be a fragment that is at least 40% (e.g., at least 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 99%) of the length of the full-length nucleic acid set forth in SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:118, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:129, SEQ ID NO:133, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:148, SEQ ID NO:150, SEQ ID NO:156, SEQ ID NO:158, SEQ ID NO:160, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:169, SEQ ID NO:171, SEQ ID NO:177, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:271, SEQ ID NO:274, SEQ ID NO:278, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:314, SEQ ID NO:317, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:327, SEQ ID NO:329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:336, SEQ ID NO:338, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:352, SEQ ID NO:354, SEQ ID NO:356, SEQ ID NO:360, SEQ ID NO:369, SEQ ID NO:371, SEQ ID NO:373, SEQ ID NO:376, SEQ ID NO:378, SEQ ID NO:380, SEQ ID NO:386, SEQ ID NO:390, SEQ ID NO:393, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID NO:416, SEQ ID NO:431, SEQ ID NO:435, SEQ ID NO:437, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:444, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:453, SEQ ID NO:458, SEQ ID NO:460, SEQ ID NO:464, SEQ ID NO:469, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:477, SEQ ID NO:482, SEQ ID NO:486, SEQ ID NO:489, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:500, SEQ ID NO:503, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:515, SEQ ID NO:517, SEQ ID NO:519, SEQ ID NO:523, SEQ ID NO:525, SEQ ID NO:528, SEQ ID NO:534, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:544, SEQ ID NO:547, SEQ ID NO:552, SEQ ID NO:554, SEQ ID NO:562, SEQ ID NO:565, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:573, SEQ ID NO:577, SEQ ID NO:580, SEQ ID NO:582, SEQ ID NO:584, SEQ ID NO:589, SEQ ID NO:592, SEQ ID NO:595, SEQ ID NO:598, SEQ ID NO:600, SEQ ID NO:602, SEQ ID NO:605, SEQ ID NO:607, SEQ ID NO:609, SEQ ID NO:611, SEQ ID NO:613, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:637, SEQ ID NO:649, SEQ ID NO:651, SEQ ID NO:655, SEQ ID NO:658, SEQ ID NO:660, SEQ ID NO:664, SEQ ID NO:670, SEQ ID NO:674, SEQ ID NO:677, SEQ ID NO:679, SEQ ID NO:681, SEQ ID NO:683, SEQ ID NO:685, SEQ ID NO:688, SEQ ID NO:694, SEQ ID NO:697, SEQ ID NO:699, SEQ ID NO:702, SEQ ID NO:704, SEQ ID NO:706, SEQ ID NO:708, SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:717, SEQ ID NO:719, SEQ ID NO:721, SEQ ID NO:723, SEQ ID NO:729, SEQ ID NO:736, SEQ ID NO:741, SEQ ID NO:743, SEQ ID NO:746, SEQ ID NO:752, SEQ ID NO:754, SEQ ID NO:759, SEQ ID NO:764, SEQ ID NO:778, SEQ ID NO:780, SEQ ID NO:785, SEQ ID NO:789, SEQ ID NO:792, SEQ ID NO:795, SEQ ID NO:797, SEQ ID NO:799, SEQ ID NO:801, SEQ ID NO:807, SEQ ID NO:810, SEQ ID NO:813, SEQ ID NO:815, SEQ ID NO:819, SEQ ID NO:821, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:829, SEQ ID NO:832, SEQ ID NO:834, SEQ ID NO:837, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:848, SEQ ID NO:851, SEQ ID NO:854, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:864, SEQ ID NO:867, SEQ ID NO:884, SEQ ID NO:889, SEQ ID NO:891, SEQ ID NO:893, SEQ ID NO:895, SEQ ID NO:897, SEQ ID NO:899, SEQ ID NO:903, SEQ ID NO:906, SEQ ID NO:911, SEQ ID NO:913, SEQ ID NO:916, SEQ ID NO:918, SEQ ID NO:920, SEQ ID NO:926, SEQ ID NO:928, SEQ ID NO:933, SEQ ID NO:935, SEQ ID NO:937, SEQ ID NO:942, SEQ ID NO:944, SEQ ID NO:958, SEQ ID NO:963, SEQ ID NO:965, SEQ ID NO:967, SEQ ID NO:972, SEQ ID NO:974, SEQ ID NO:979, SEQ ID NO:981, SEQ ID NO:993, SEQ ID NO:1006, SEQ ID NO:1010, SEQ ID NO:1015, SEQ ID NO:1027, SEQ ID NO:1030, SEQ ID NO:1034, SEQ ID NO:1049, SEQ ID NO:1051, SEQ ID NO:1054, SEQ ID NO:1057, SEQ ID NO:1059, SEQ ID NO:1061, SEQ ID NO:1063, SEQ ID NO:1067, SEQ ID NO:1070, SEQ ID NO:1077, SEQ ID NO:1080, SEQ ID NO:1082, SEQ ID NO:1084, SEQ ID NO:1086, SEQ ID NO:1090, SEQ ID NO:1093, SEQ ID NO:1095, SEQ ID NO:1097, SEQ ID NO:1103, SEQ ID NO:1108, SEQ ID NO:1116, SEQ ID NO:1121, SEQ ID NO:1124, SEQ ID NO:1128, SEQ ID NO:1130, SEQ ID NO:1133, SEQ ID NO:1135, SEQ ID NO:1138, SEQ ID NO:1142, SEQ ID NO:1148, SEQ ID NO:1155, SEQ ID NO:1158, SEQ ID NO:1160, SEQ ID NO:1162, SEQ ID NO:1164, SEQ ID NO:1170, SEQ ID NO:1172, SEQ ID NO:1175, SEQ ID NO:1182, SEQ ID NO:1184, SEQ ID NO:1208, SEQ ID NO:1210, SEQ ID NO:1212, SEQ ID NO:1214, SEQ ID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1236, SEQ ID NO:1238, SEQ ID NO:1240, SEQ ID NO:1242, SEQ ID NO:1244, SEQ ID NO:1246, SEQ ID NO:1248, SEQ ID NO:1250, SEQ ID NO:1252, SEQ ID NO:1254, SEQ ID NO:1256, SEQ ID NO:1258, SEQ ID NO:1260, SEQ ID NO:1262, SEQ ID NO:1264, SEQ ID NO:1266, SEQ ID NO:1268, SEQ ID NO:1270, SEQ ID NO:1272, SEQ ID NO:1274, SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1282, SEQ ID NO:1284, SEQ ID NO:1291, SEQ ID NO:1293, SEQ ID NO:1295, SEQ ID NO:1297, SEQ ID NO:1299, SEQ ID NO:1301, SEQ ID NO:1310, SEQ ID NO:1312, SEQ ID NO:1314, SEQ ID NO:1316, SEQ ID NO:1318, SEQ ID NO:1320, SEQ ID NO:1322, SEQ ID NO:1324, SEQ ID NO:1326, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1332, SEQ ID NO:1334, SEQ ID NO:1336, SEQ ID NO:1338, SEQ ID NO:1340, SEQ ID NO:1342, SEQ ID NO:1344, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1356, SEQ ID NO:1358, SEQ ID NO:1360, SEQ ID NO:1368, SEQ ID NO:1370, SEQ ID NO:1372, SEQ ID NO:1374, SEQ ID NO:1376, SEQ ID NO:1378, SEQ ID NO:1380, SEQ ID NO:1382, SEQ ID NO:1384, SEQ ID NO:1386, SEQ ID NO:1388, SEQ ID NO:1390, SEQ ID NO:1392, SEQ ID NO:1394, SEQ ID NO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1402, SEQ ID NO:1404, SEQ ID NO:1411, SEQ ID NO:1413, SEQ ID NO:1416, SEQ ID NO:1418, SEQ ID NO:1420, SEQ ID NO:1422, SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1434, SEQ ID NO:1435, SEQ ID NO:1443, SEQ ID NO:1464, SEQ ID NO:1466, SEQ ID NO:1468, SEQ ID NO:1470, SEQ ID NO:1472, SEQ ID NO:1474, SEQ ID NO:1476, SEQ ID NO:1478, SEQ ID NO:1480, SEQ ID NO:1482, SEQ ID NO:1484, SEQ ID NO:1486, SEQ ID NO:1492, SEQ ID NO:1501, SEQ ID NO:1503, SEQ ID NO:1517, SEQ ID NO:1519, SEQ ID NO:1521, SEQ ID NO:1523, SEQ ID NO:1525, SEQ ID NO:1527, SEQ ID NO:1535, SEQ ID NO:1537, SEQ ID NO:1539, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1549, SEQ ID NO:1551, SEQ ID NO:1553, SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1563, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID NO:1569, SEQ ID NO:1572, SEQ ID NO:1574, SEQ ID NO:1576, SEQ ID NO:1578, SEQ ID NO:1580, SEQ ID NO:1582, SEQ ID NO:1584, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1594, SEQ ID NO:1609, SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1619, SEQ ID NO:1623, SEQ ID NO:1625, SEQ ID NO:1627, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1636, SEQ ID NO:1652, SEQ ID NO:1656, SEQ ID NO:1658, SEQ ID NO:1660, SEQ ID NO:1662, SEQ ID NO:1664, SEQ ID NO:1666, SEQ ID NO:1668, SEQ ID NO:1670, SEQ ID NO:1672, SEQ ID NO:1674, SEQ ID NO:1680, SEQ ID NO:1682, SEQ ID NO:1691, SEQ ID NO:1693, SEQ ID NO:1695, SEQ ID NO:1697, SEQ ID NO:1699, SEQ ID NO:1701, SEQ ID NO:1703, SEQ ID NO:1705, SEQ ID NO:1707, SEQ ID NO:1709, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1715, SEQ ID NO:1717, SEQ ID NO:1719, SEQ ID NO:1721, SEQ ID NO:1723, SEQ ID NO:1725, SEQ ID NO:1727, SEQ ID NO:1732, SEQ ID NO:1734, SEQ ID NO:1748, SEQ ID NO:1751, SEQ ID NO:1766, SEQ ID NO:1776, SEQ ID NO:1778, SEQ ID NO:1780, SEQ ID NO:1782, SEQ ID NO:1784, SEQ ID NO:1805, SEQ ID NO:1821, SEQ ID NO:1823, SEQ ID NO:1825, SEQ ID NO:1827, SEQ ID NO:1829, SEQ ID NO:1831, SEQ ID NO:1833, SEQ ID NO:1835, SEQ ID NO:1837, SEQ ID NO:1839, SEQ ID NO:1841, SEQ ID NO:1843, SEQ ID NO:1845, SEQ ID NO:1847, SEQ ID NO:1849, SEQ ID NO:1851, SEQ ID NO:1853, SEQ ID NO:1855, SEQ ID NO:1857, SEQ ID NO:1859, SEQ ID NO:1861, SEQ ID NO:1863, SEQ ID NO:1865, SEQ ID NO:1867, SEQ ID NO:1869, SEQ ID NO:1871, SEQ ID NO:1873, SEQ ID NO:1875, SEQ ID NO:1877, SEQ ID NO:1879, SEQ ID NO:1881, SEQ ID NO:1883, SEQ ID NO:1885, SEQ ID NO:1887, SEQ ID NO:1889, SEQ ID NO:1891, SEQ ID NO:1896, SEQ ID NO:1898, SEQ ID NO:1900, SEQ ID NO:1903, SEQ ID NO:1905, SEQ ID NO:1907, SEQ ID NO:1919, SEQ ID NO:1920, SEQ ID NO:2060, SEQ ID NO:2062, SEQ ID NO:2064, SEQ ID NO:2084, SEQ ID NO:2088, SEQ ID NO:2090, SEQ ID NO:2092, SEQ ID NO:2094, SEQ ID NO:2096, SEQ ID NO:2098, SEQ ID NO:2100, SEQ ID NO:2102, SEQ ID NO:2104, SEQ ID NO:2106, SEQ ID NO:2108, SEQ ID NO:2110, SEQ ID NO:2112, SEQ ID NO:2114, SEQ ID NO:2116, SEQ ID NO:2118, SEQ ID NO:2120, SEQ ID NO:2122, SEQ ID NO:2124, SEQ ID NO:2126, SEQ ID NO:2128, SEQ ID NO:2130, SEQ ID NO:2132, SEQ ID NO:2134, SEQ ID NO:2136, SEQ ID NO:2138, SEQ ID NO:2140, SEQ ID NO:2142, SEQ ID NO:2144, SEQ ID NO:2146, SEQ ID NO:2148, SEQ ID NO:2150, SEQ ID NO:2152, SEQ ID NO:2154, SEQ ID NO:2156, SEQ ID NO:2158, SEQ ID NO:2160, SEQ ID NO:2161, SEQ ID NO:2163, SEQ ID NO:2165, SEQ ID NO:6167, SEQ ID NO:2169, SEQ ID NO:2171, SEQ ID NO:2173, SEQ ID NO:2175, SEQ ID NO:2177, SEQ ID NO:2179, SEQ ID NO:2181, SEQ ID NO:2183, SEQ ID NO:2185, SEQ ID NO:2187, SEQ ID NO:2189, SEQ ID NO:2191, SEQ ID NO:2193, SEQ ID NO:2195, SEQ ID NO:2197, SEQ ID NO:2199, SEQ ID NO:2201, SEQ ID NO:2203, SEQ ID NO:2205, SEQ ID NO:2207, SEQ ID NO:2209, SEQ ID NO:2211, SEQ ID NO:2213, SEQ ID NO:2215, SEQ ID NO:2217, SEQ ID NO:2219, SEQ ID NO:2221, SEQ ID NO:2223, SEQ ID NO:2225, SEQ ID NO:2227, SEQ ID NO:2229, SEQ ID NO:2231, SEQ ID NO:2233, SEQ ID NO:2235, SEQ ID NO:2237, SEQ ID NO:2239, SEQ ID NO:2241, SEQ ID NO:2243, SEQ ID NO:2245, SEQ ID NO:2247, SEQ ID NO:2249, SEQ ID NO:2251, SEQ ID NO:2253, SEQ ID NO:2255, SEQ ID NO:2257, SEQ ID NO:2259, SEQ ID NO:2261, SEQ ID NO:2263, SEQ ID NO:2265, SEQ ID NO:2267, SEQ ID NO:2269, SEQ ID NO:2271, SEQ ID NO:2273, SEQ ID NO:2275, SEQ ID NO:2277, SEQ ID NO:2279, SEQ ID NO:2281, SEQ ID NO:2283, SEQ ID NO:2285, SEQ ID NO:2287, SEQ ID NO:2289, SEQ ID NO:2291, SEQ ID NO:2293, SEQ ID NO:2295, SEQ ID NO:2297, SEQ ID NO:2299, SEQ ID NO:2301, SEQ ID NO:2303, SEQ ID NO:2305, SEQ ID NO:2307, SEQ ID NO:2309, SEQ ID NO:2311, SEQ ID NO:2313, SEQ ID NO:2315, SEQ ID NO:2317, SEQ ID NO:2319, SEQ ID NO:2321, SEQ ID NO:2323, SEQ ID NO:2325, SEQ ID NO:2327, SEQ ID NO:2329, SEQ ID NO:2331, SEQ ID NO:2333, SEQ ID NO:2335, SEQ ID NO:2337, SEQ ID NO:2339, SEQ ID NO:2341, SEQ ID NO:2343, SEQ ID NO:2345, SEQ ID NO:2347, and SEQ ID NO:2349-2690. In some cases, a recombinant nucleic acid construct can include a nucleic acid comprising a coding sequence, a gene, or a fragment of a coding sequence or gene in an antisense orientation so that the antisense strand of RNA is transcribed.

It will be appreciated that a number of nucleic acids can encode a polypeptide having a particular amino acid sequence. The degeneracy of the genetic code is well known to the art; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino acid. For example, codons in the coding sequence for a given regulatory protein can be modified such that optimal expression in a particular plant species is obtained, using appropriate codon bias tables for that species.

A nucleic acid also can comprise a nucleotide sequence corresponding to any of the regulatory regions as set forth in SEQ ID NOs:1-94 or SEQ ID NOs:1909-1918. In some cases, a nucleic acid can comprise a nucleotide sequence corresponding to any of the regulatory regions set forth in SEQ ID NOs:1-94 or SEQ ID NOs:1909-1918, and a coding sequence that encodes any of the regulatory proteins set forth in SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, or SEQ ID NO:2087.

The terms “nucleic acid” and “polynucleotide” are used interchangeably herein, and refer both to RNA and DNA, including cDNA, genomic DNA, synthetic DNA, and DNA (or RNA) containing nucleic acid analogs. Polynucleotides can have any three-dimensional structure. A nucleic acid can be double-stranded or single-stranded (i.e., a sense strand or an antisense strand). Non-limiting examples of polynucleotides include genes, gene fragments, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, siRNA, micro-RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers, as well as nucleic acid analogs.

An isolated nucleic acid can be, for example, a naturally-occurring DNA molecule, provided one of the nucleic acid sequences normally found immediately flanking that DNA molecule in a naturally-occurring genome is removed or absent. Thus, an isolated nucleic acid includes, without limitation, a DNA molecule that exists as a separate molecule, independent of other sequences (e.g., a chemically synthesized nucleic acid, or a cDNA or genomic DNA fragment produced by the polymerase chain reaction (PCR) or restriction endonuclease treatment). An isolated nucleic acid also refers to a DNA molecule that is incorporated into a vector, an autonomously replicating plasmid, a virus, or into the genomic DNA of a prokaryote or eukaryote. In addition, an isolated nucleic acid can include an engineered nucleic acid such as a DNA molecule that is part of a hybrid or fusion nucleic acid. A nucleic acid existing among hundreds to millions of other nucleic acids within, for example, cDNA libraries or genomic libraries, or gel slices containing a genomic DNA restriction digest, is not to be considered an isolated nucleic acid.

Isolated nucleic acid molecules can be produced by standard techniques. For example, polymerase chain reaction (PCR) techniques can be used to obtain an isolated nucleic acid containing a nucleotide sequence described herein. PCR can be used to amplify specific sequences from DNA as well as RNA, including sequences from total genomic DNA or total cellular RNA. Various PCR methods are described, for example, in PCR Primer: A Laboratory Manual, Dieffenbach and Dveksler, eds., Cold Spring Harbor Laboratory Press, 1995. Generally, sequence information from the ends of the region of interest or beyond is employed to design oligonucleotide primers that are identical or similar in sequence to opposite strands of the template to be amplified. Various PCR strategies also are available by which site-specific nucleotide sequence modifications can be introduced into a template nucleic acid. Isolated nucleic acids also can be chemically synthesized, either as a single nucleic acid molecule (e.g., using automated DNA synthesis in the 3′ to 5′ direction using phosphoramidite technology) or as a series of oligonucleotides. For example, one or more pairs of long oligonucleotides (e.g., >100 nucleotides) can be synthesized that contain the desired sequence, with each pair containing a short segment of complementarity (e.g., about 15 nucleotides) such that a duplex is formed when the oligonucleotide pair is annealed. DNA polymerase is used to extend the oligonucleotides, resulting in a single, double-stranded nucleic acid molecule per oligonucleotide pair, which then can be ligated into a vector. Isolated nucleic acids of the invention also can be obtained by mutagenesis of, e.g., a naturally occurring DNA.

As used herein, the term “percent sequence identity” refers to the degree of identity between any given reference sequence and a subject sequence. A subject sequence typically has a length that is more than 80%, e.g., more than 82%, 85%, 87%, 89%, 90%, 93%, 95%, 97%, 99%, 100%, 105%, 110%, 115%, or 120%, of the length of the reference sequence. A reference nucleic acid or amino acid sequence is aligned to one or more subject nucleic acid or amino acid sequences using the computer program ClustalW (version 1.83, default parameters), which allows alignments of nucleic acid or protein sequences to be carried out across their entire length (global alignment). Chema et al., Nucleic Acids Res., 31(13):3497-500 (2003).

ClustalW calculates the best match between a reference and one or more subject sequences, and aligns them so that identities, similarities and differences can be determined. Gaps of one or more residues can be inserted into a reference sequence, a subject sequence, or both, to maximize sequence alignments. For fast pairwise alignment of nucleic acid sequences, the following default parameters are used: word size: 2; window size: 4; scoring method: percentage; number of top diagonals: 4; and gap penalty: 5. For multiple alignment of nucleic acid sequences, the following parameters are used: gap opening penalty: 10.0; gap extension penalty: 5.0; and weight transitions: yes. For fast pairwise alignment of protein sequences, the following parameters are used: word size: 1; window size: 5; scoring method: percentage; number of top diagonals: 5; gap penalty: 3. For multiple alignment of protein sequences, the following parameters are used: weight matrix: blosum; gap opening penalty: 10.0; gap extension penalty: 0.05; hydrophilic gaps: on; hydrophilic residues: Gly, Pro, Ser, Asn, Asp, Gln, Glu, Arg, and Lys; residue-specific gap penalties: on. The output is a sequence alignment that reflects the relationship between sequences. ClustalW can be run, for example, at the Baylor College of Medicine Search Launcher site (searchlauncher.bcm.tmc.edu/multi-align/multi-align.html) and at the European Bioinformatics Institute site on the World Wide Web (ebi.ac.uk/clustalw).

To determine a percent identity between a reference sequence and a subject sequence, ClustalW divides the number of identities in the best alignment by the number of residues compared (gap positions are excluded), and multiplies the result by 100. The output is the percent identity of the subject sequence with respect to the reference sequence. It is noted that the percent identity value can be rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 are rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded up to 78.2.

The term “exogenous” with respect to a nucleic acid indicates that the nucleic acid is part of a recombinant nucleic acid construct, or is not in its natural environment. For example, an exogenous nucleic acid can be a sequence from one species introduced into another species, i.e., a heterologous nucleic acid. Typically, such an exogenous nucleic acid is introduced into the other species via a recombinant nucleic acid construct. An exogenous nucleic acid can also be a sequence that is native to an organism and that has been reintroduced into cells of that organism. An exogenous nucleic acid that includes a native sequence can often be distinguished from the naturally occurring sequence by the presence of non-natural sequences linked to the exogenous nucleic acid, e.g., non-native nucleic acid sequences flanking a native sequence in a recombinant nucleic acid construct. In addition, stably transformed exogenous nucleic acids typically are integrated at positions other than the position where the native sequence is found. It will be appreciated that an exogenous nucleic acid may have been introduced into a progenitor and not into the cell under consideration. For example, a transgenic plant containing an exogenous nucleic acid can be the progeny of a cross between a stably transformed plant and a non-transgenic plant. Such progeny are considered to contain the exogenous nucleic acid.

Similarly, a regulatory protein can be endogenous or exogenous to a particular plant or plant cell. Exogenous regulatory proteins, therefore, can include proteins that are native to a plant or plant cell, but that are expressed in a plant cell via a recombinant nucleic acid construct, e.g., a Panicum plant transformed with a recombinant nucleic acid construct encoding a Panicum transcription factor.

Likewise, a regulatory region can be exogenous or endogenous to a plant or plant cell. An exogenous regulatory region is a regulatory region that is part of a recombinant nucleic acid construct, or is not in its natural environment. For example, a Nicotiana promoter present on a recombinant nucleic acid construct is an exogenous regulatory region when a Nicotiana plant cell is transformed with the construct.

A transgenic plant or plant cell in which the amount and/or rate of biosynthesis of one or more sequences of interest is modulated includes at least one recombinant nucleic acid construct, e.g., a nucleic acid construct comprising a nucleic acid encoding a regulatory protein or a nucleic acid construct comprising a regulatory region as described herein. In certain cases, more than one recombinant nucleic acid construct can be included (e.g., two, three, four, five, six, or more recombinant nucleic acid constructs). For example, two recombinant nucleic acid constructs can be included, where one construct includes a nucleic acid encoding one regulatory protein, and another construct includes a nucleic acid encoding a second regulatory protein. In some cases, one construct can include a nucleic acid encoding one regulatory protein, while another includes a regulatory region. In some cases, a plant cell can include a recombinant nucleic acid construct comprising a nucleic acid encoding a regulatory protein and further comprising a regulatory region that associates with the regulatory protein. In such cases, additional recombinant nucleic acid constructs can also be included in the plant cell, e.g., containing additional regulatory proteins and/or regulatory regions.

Vectors containing nucleic acids such as those described herein also are provided. A “vector” is a replicon, such as a plasmid, phage, or cosmid, into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. Generally, a vector is capable of replication when associated with the proper control elements. Suitable vector backbones include, for example, those routinely used in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs, or PACs. The term “vector” includes cloning and expression vectors, as well as viral vectors and integrating vectors. An “expression vector” is a vector that includes a regulatory region. Suitable expression vectors include, without limitation, plasmids and viral vectors derived from, for example, bacteriophage, baculoviruses, and retroviruses. Numerous vectors and expression systems are commercially available from such corporations as Novagen (Madison, Wis.), Clontech (Mountain View, Calif.), Stratagene (La Jolla, Calif.), and Invitrogen/Life Technologies (Carlsbad, Calif.).

The vectors provided herein also can include, for example, origins of replication, scaffold attachment regions (SARs), and/or markers. A marker gene can confer a selectable phenotype on a plant cell. For example, a marker can confer biocide resistance, such as resistance to an antibiotic (e.g., kanamycin, G418, bleomycin, or hygromycin), or an herbicide (e.g., chlorosulfuron or phosphinothricin). In addition, an expression vector can include a tag sequence designed to facilitate manipulation or detection (e.g., purification or localization) of the expressed polypeptide. Tag sequences, such as green fluorescent protein (GFP), glutathione S-transferase (GST), polyhistidine, c-myc, hemagglutinin, or Flag™ tag (Kodak, New Haven, Conn.) sequences typically are expressed as a fusion with the encoded polypeptide. Such tags can be inserted anywhere within the polypeptide, including at either the carboxyl or amino terminus.

As described herein, plant cells can be transformed with a recombinant nucleic acid construct to express a polypeptide of interest. The polypeptide can then be extracted and purified using techniques known to those having ordinary skill in the art.

Regulatory Regions

The term “regulatory region” refers to a nucleic acid having nucleotide sequences that influence transcription or translation initiation and rate, and stability and/or mobility of a transcription or translation product. Regulatory regions include, without limitation, promoter sequences, enhancer sequences, response elements, protein recognition sites, inducible elements, protein binding sequences, 5′ and 3′ untranslated regions (UTRs), transcriptional start sites, termination sequences, polyadenylation sequences, introns, and combinations thereof.

When a regulatory region is operably linked to a sequence of interest, the regulatory region is selected from among those that are associated with a regulatory protein described herein. Such a regulatory region is referred to herein as an “associated regulatory region.” For example, a recombinant nucleic acid construct can comprise a regulatory region from Table 2 (SEQ ID NOs:1909-1918) operably linked to a sequence of interest. Expression of the sequence of interest is thereby dependent on expression of a regulatory protein(s) that is associated with that regulatory region. Associations between regulatory proteins and regulatory regions are set forth in Table 4. In some embodiments, a regulatory region useful in the compositions and methods described herein has 80% or greater, e.g., 85%, 90%, 95%, 97%, 98%, 99%, or 100%, sequence identity to a regulatory region set forth in SEQ ID NOs:1909-1918.

To control the expression pattern of an associated regulatory protein itself, and thereby indirectly modulate expression of a sequence of interest, another regulatory region, which can be the same as or different from the associated regulatory region, is operably linked to a coding sequence for that regulatory protein. The choice of regulatory regions is influenced by the tissues and developmental stages in which one desires expression of the regulatory protein and/or sequence of interest to occur, but is otherwise not limited in any substantial way. For example, if one desires expression of the sequence of interest to occur in vegetative tissues, the associated regulatory protein can be broadly expressed, e.g., under the direction of a p326 promoter, or more precisely expressed, e.g., under the direction of a YP0144 photosynthetic tissue promoter. In either case, the regulatory protein can directly or indirectly affect expression of a sequence of interest operably linked to an associated regulatory region. In some cases, a regulatory protein can be expressed under the direction of a cell type- or tissue-preferential promoter, such as a cell type- or tissue-preferential promoter described below.

As used herein, the term “operably linked” refers to positioning of a regulatory region and a sequence to be transcribed in a nucleic acid so as to influence transcription or translation of such a sequence. For example, to bring a coding sequence under the control of a regulatory region, the translation initiation site of the translational reading frame of the polypeptide is typically positioned between one and about fifty nucleotides downstream of the regulatory region. A regulatory region can, however, be positioned as much as about 5,000 nucleotides upstream of the translation initiation site, or about 2,000 nucleotides upstream of the transcription start site. A regulatory region typically comprises at least a core (basal) promoter. A regulatory region also may include at least one control element, such as an enhancer sequence, an upstream element or an upstream activation region (UAR). For example, a suitable enhancer is a cis-regulatory element (−212 to −154) from the upstream region of the octopine synthase (ocs) gene. Fromm et al., The Plant Cell, 1:977-984 (1989). The choice of regulatory regions to be included depends upon several factors, including, but not limited to, efficiency, selectability, inducibility, desired expression level, and cell- or tissue-preferential expression. It is a routine matter for one of skill in the art to modulate the expression of a coding sequence by appropriately selecting and positioning regulatory regions relative to the coding sequence.

Some suitable regulatory regions initiate transcription only, or predominantly, in certain cell types. For example, a promoter that is active predominantly in a reproductive tissue (e.g., fruit, ovule, or inflorescence) can be used. Thus, as used herein a cell type- or tissue-preferential promoter is one that drives expression preferentially in the target tissue, but may also lead to some expression in other cell types or tissues as well. Methods for identifying and characterizing regulatory regions in plant genomic DNA include, for example, those described in the following references: Jordano et al., Plant Cell, 1:855-866 (1989); Bustos et al., Plant Cell, 1:839-854 (1989); Green et al., EMBO J., 7:4035-4044 (1988); Meier et al., Plant Cell, 3:309-316 (1991); and Zhang et al., Plant Physiology, 110:1069-1079 (1996).

Examples of various classes of regulatory regions are described below. Some of the regulatory regions indicated below as well as additional regulatory regions are described in more detail in U.S. Patent Application Ser. Nos. 60/505,689; 60/518,075; 60/544,771; 60/558,869; 60/583,691; 60/619,181; 60/637,140; 60/757,544; 60/776,307; 10/957,569; 11/058,689; 11/172,703; 11/208,308; 11/274,890; 60/583,609; 60/612,891; 11/097,589; 11/233,726; 11/408,791; 11/414,142; 10/950,321; 11/360,017; PCT/US05/011105; PCT/US05/034308; and PCT/US05/23639. Nucleotide sequences of regulatory regions are set forth in SEQ ID NOs:1-94 and SEQ ID NOs:1909-1918. It will be appreciated that a regulatory region may meet criteria for one classification based on its activity in one plant species, and yet meet criteria for a different classification based on its activity in another plant species.

Broadly Expressing Promoters

A promoter can be said to be “broadly expressing” when it promotes transcription in many, but not necessarily all, plant tissues. For example, a broadly expressing promoter can promote transcription of an operably linked sequence in one or more of the shoot, shoot tip (apex), and leaves, but weakly or not at all in tissues such as roots or stems. As another example, a broadly expressing promoter can promote transcription of an operably linked sequence in one or more of the stem, shoot, shoot tip (apex), and leaves, but can promote transcription weakly or not at all in tissues such as reproductive tissues of flowers and developing seeds. Non-limiting examples of broadly expressing promoters that can be included in the nucleic acid constructs provided herein include the p326 (SEQ ID NO:76), YP0144 (SEQ ID NO:55), YP0190 (SEQ ID NO:59), p13879 (SEQ ID NO:75), YP0050 (SEQ ID NO:35), p32449 (SEQ ID NO:77), 21876 (SEQ ID NO:1), YP0158 (SEQ ID NO:57), YP0214 (SEQ ID NO:61), YP0380 (SEQ ID NO:70), PT0848 (SEQ ID NO:26), and PT0633 (SEQ ID NO:7) promoters. Additional examples include the cauliflower mosaic virus (CaMV) 35S promoter, the mannopine synthase (MAS) promoter, the 1′ or 2′ promoters derived from T-DNA of Agrobacterium tumefaciens, the figwort mosaic virus 34S promoter, actin promoters such as the rice actin promoter, and ubiquitin promoters such as the maize ubiquitin-1 promoter. In some cases, the CaMV 35S promoter is excluded from the category of broadly expressing promoters.

Root Promoters

Root-active promoters confer transcription in root tissue, e.g., root endodermis, root epidermis, or root vascular tissues. In some embodiments, root-active promoters are root-preferential promoters, i.e., confer transcription only or predominantly in root tissue. Root-preferential promoters include the YP0128 (SEQ ID NO:52), YP0275 (SEQ ID NO:63), PT0625 (SEQ ID NO:6), PT0660 (SEQ ID NO:9), PT0683 (SEQ ID NO:14), and PT0758 (SEQ ID NO:22) promoters. Other root-preferential promoters include the PT0613 (SEQ ID NO:5), PT0672 (SEQ ID NO:11), PT0688 (SEQ ID NO:15), and PT0837 (SEQ ID NO:24) promoters, which drive transcription primarily in root tissue and to a lesser extent in ovules and/or seeds. Other examples of root-preferential promoters include the root-specific subdomains of the CaMV 35S promoter (Lam et al., Proc. Natl. Acad. Sci. USA, 86:7890-7894 (1989)), root cell specific promoters reported by Conkling et al., Plant Physiol., 93:1203-1211 (1990), and the tobacco RD2 promoter.

Maturing Endosperm Promoters

In some embodiments, promoters that drive transcription in maturing endosperm can be useful. Transcription from a maturing endosperm promoter typically begins after fertilization and occurs primarily in endosperm tissue during seed development and is typically highest during the cellularization phase. Most suitable are promoters that are active predominantly in maturing endosperm, although promoters that are also active in other tissues can sometimes be used. Non-limiting examples of maturing endosperm promoters that can be included in the nucleic acid constructs provided herein include the napin promoter, the Arcelin-5 promoter, the phaseolin promoter (Bustos et al., Plant Cell, 1(9):839-853 (1989)), the soybean trypsin inhibitor promoter (Riggs et al., Plant Cell, 1(6):609-621 (1989)), the ACP promoter (Baerson et al., Plant Mol. Biol., 22(2):255-267 (1993)), the stearoyl-ACP desaturase promoter (Slocombe et al., Plant Physiol., 104(4):167-176 (1994)), the soybean α′ subunit of β-conglycinin promoter (Chen et al., Proc. Natl. Acad. Sci. USA, 83:8560-8564 (1986)), the oleosin promoter (Hong et al., Plant Mol. Biol., 34(3):549-555 (1997)), and zein promoters, such as the 15 kD zein promoter, the 16 kD zein promoter, 19 kD zein promoter, 22 kD zein promoter and 27 kD zein promoter. Also suitable are the Osgt-1 promoter from the rice glutelin-1 gene (Zheng et al., Mol. Cell Biol., 13:5829-5842 (1993)), the beta-amylase promoter, and the barley hordein promoter. Other maturing endosperm promoters include the YP0092 (SEQ ID NO:38), PT0676 (SEQ ID NO:12), and PT0708 (SEQ ID NO:17) promoters.

Ovary Tissue Promoters

Promoters that are active in ovary tissues such as the ovule wall and mesocarp can also be useful, e.g., a polygalacturonidase promoter, the banana TRX promoter, the melon actin promoter, YP0396 (SEQ ID NO:74), and PT0623 (SEQ ID NO:94). Examples of promoters that are active primarily in ovules include YP0007 (SEQ ID NO:30), YP0111 (SEQ ID NO:46), YP0092 (SEQ ID NO:38), YP0103 (SEQ ID NO:43), YP0028 (SEQ ID NO:33), YP0121 (SEQ ID NO:51), YP0008 (SEQ ID NO:31), YP0039 (SEQ ID NO:34), YP0115 (SEQ ID NO:47), YP0119 (SEQ ID NO:49), YP0120 (SEQ ID NO:50), and YP0374 (SEQ ID NO:68).

Embryo Sac/Early Endosperm Promoters

To achieve expression in embryo sac/early endosperm, regulatory regions can be used that are active in polar nuclei and/or the central cell, or in precursors to polar nuclei, but not in egg cells or precursors to egg cells. Most suitable are promoters that drive expression only or predominantly in polar nuclei or precursors thereto and/or the central cell. A pattern of transcription that extends from polar nuclei into early endosperm development can also be found with embryo sac/early endosperm-preferential promoters, although transcription typically decreases significantly in later endosperm development during and after the cellularization phase. Expression in the zygote or developing embryo typically is not present with embryo sac/early endosperm promoters.

Promoters that may be suitable include those derived from the following genes: Arabidopsis viviparous-1 (see, GenBank No. U93215); Arabidopsis atmycl (see, Urao (1996) Plant Mol. Biol., 32:571-57; Conceicao (1994) Plant, 5:493-505); Arabidopsis FIE (GenBank No. AF129516); Arabidopsis MEA; Arabidopsis FIS2 (GenBank No. AF096096); and FIE 1.1 (U.S. Pat. No. 6,906,244). Other promoters that may be suitable include those derived from the following genes: maize MAC1 (see, Sheridan (1996) Genetics, 142:1009-1020); maize Cat3 (see, GenBank No. L05934; Abler (1993) Plant Mol. Biol., 22:10131-1038). Other promoters include the following Arabidopsis promoters: YP0039 (SEQ ID NO:34), YP0101 (SEQ ID NO:41), YP0102 (SEQ ID NO:42), YP0110 (SEQ ID NO:45), YP0117 (SEQ ID NO:48), YP0119 (SEQ ID NO:49), YP0137 (SEQ ID NO:53), DME, YP0285 (SEQ ID NO:64), and YP0212 (SEQ ID NO:60). Other promoters that may be useful include the following rice promoters: p530c10 (SEQ ID NO:79), pOsFIE2-2 (SEQ ID NO:80), pOsMEA (SEQ ID NO:81), pOsYp102 (SEQ ID NO:82), and pOsYp285 (SEQ ID NO:83).

Embryo Promoters

Regulatory regions that preferentially drive transcription in zygotic cells following fertilization can provide embryo-preferential expression. Most suitable are promoters that preferentially drive transcription in early stage embryos prior to the heart stage, but expression in late stage and maturing embryos is also suitable. Embryo-preferential promoters include the barley lipid transfer protein (Ltp1) promoter (Plant Cell Rep (2001) 20:647-654), YP0097 (SEQ ID NO:40), YP0107 (SEQ ID NO:44), YP0088 (SEQ ID NO:37), YP0143 (SEQ ID NO:54), YP0156 (SEQ ID NO:56), PT0650 (SEQ ID NO:8), PT0695 (SEQ ID NO:16), PT0723 (SEQ ID NO:19), PT0838 (SEQ ID NO:25), PT0879 (SEQ ID NO:28), and PT0740 (SEQ ID NO:20).

Photosynthetic Tissue Promoters

Promoters active in photosynthetic tissue confer transcription in green tissues such as leaves and stems. Most suitable are promoters that drive expression only or predominantly in such tissues. Examples of such promoters include the ribulose-1,5-bisphosphate carboxylase (RbcS) promoters such as the RbcS promoter from eastern larch (Larix laricina), the pine cab6 promoter (Yamamoto et al., Plant Cell Physiol., 35:773-778 (1994)), the Cab-1 promoter from wheat (Fejes et al., Plant Mol. Biol., 15:921-932 (1990)), the CAB-1 promoter from spinach (Lubberstedt et al., Plant Physiol., 104:997-1006 (1994)), the cab1R promoter from rice (Luan et al., Plant Cell, 4:971-981 (1992)), the pyruvate orthophosphate dikinase (PPDK) promoter from corn (Matsuoka et al., Proc. Natl. Acad. Sci. USA, 90:9586-9590 (1993)), the tobacco Lhcb1*2 promoter (Cerdan et al., Plant Mol. Biol., 33:245-255 (1997)), the Arabidopsis thaliana SUC2 sucrose-H+ symporter promoter (Truernit et al., Planta, 196:564-570 (1995)), and thylakoid membrane protein promoters from spinach (psaD, psaF, psaE, PC, FNR, atpC, atpD, cab, rbcS). Other photosynthetic tissue promoters include PT0535 (SEQ ID NO:3), PT0668 (SEQ ID NO:2), PT0886 (SEQ ID NO:29), YP0144 (SEQ ID NO:55), YP0380 (SEQ ID NO:70) and PT0585 (SEQ ID NO:4).

Lignin Biosynthesis Promoters

Lignin biosynthesis promoters are promoters that drive transcription of nucleic acids encoding enzymes involved in lignin biosynthesis. Such enzymes include, without limitation, 4-(hydroxy)cinnamoyl CoA ligase (EC 6.2.1.12), ferulate 5-hydroxylase, cinnamoyl CoA reductase (EC 1.2.1.44), cinnamate 4-hydroxylase (EC 1.14.13.11), and cinnamyl alcohol dehydrogenase (EC 1.1.1.195). Examples of lignin biosynthesis promoters from Populus are set forth in SEQ ID NOs:1909-1918. Other examples of lignin biosynthesis promoters include promoters of the switchgrass (Panicum virgatum), rice (Oryza sativa), corn (Zea mays), and wheat (Triticum aestivum) homologs of the Populus cinnamate 4-hydroxylase, caffeoyl-CoA O-methyltransferase, and caffeic acid O-methyltransferase genes. Also suitable are promoters of Arabidopsis genes encoding phenylalanin ammonia lyase (genomic locus At3g10340), trans-cinnamate 4-hydroxylase (genomic locus At2g30490), 4-coumarate:CoA ligase (genomic locus At1g51680), hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase (genomic locus At5g48930), p-Coumarate 3-hydroxylase (genomic locus At2g40890), caffeoyl-CoA 3-O-methyltransferase (genomic locus At4g34050), cinnamoyl CoA reductase (genomic locus At1g15950), ferulate 5-hydroxylase (genomic locus At4g36220), caffeic acid O-methyltransferase (genomic locus At5g54160), and cinnamyl alcohol dehydrogenase (genomic locus At4g34230).

Cell Wall Related Promoters

Useful promoters also include cell wall related promoters, such as cellulose biosynthesis promoters. Cellulose biosynthesis promoters are promoters that drive transcription of nucleic acids encoding enzymes involved in cellulose biosynthesis. Examples of cellulose biosynthesis promoters include the promoter of the rice cellulose synthase gene (genomic locus Os08g25710), the promoter of the rice cellulose synthase gene (genomic locus Os08g06380), and the promoter of the rice cellulose synthase-like A2 gene (genomic locus Os10g26630).

Vascular Tissue Promoters

Examples of promoters that have high or preferential activity in vascular bundles include YP0087 (SEQ ID NO:86), YP0093 (SEQ ID NO:87), YP0108 (SEQ ID NO:88), YP0022 (SEQ ID NO:89), and YP0080 (SEQ ID NO:90). Other vascular tissue-preferential promoters include the glycine-rich cell wall protein GRP 1.8 promoter (Keller and Baumgartner, Plant Cell, 3(10):1051-1061 (1991)), the Commelina yellow mottle virus (CoYMV) promoter (Medberry et al., Plant Cell, 4(2):185-192 (1992)), and the rice tungro bacilliform virus (RTBV) promoter (Dai et al., Proc. Natl. Acad. Sci. USA, 101(2):687-692 (2004)). Promoters having preferential activity in the phloem region (e.g., primary phloem cells, companion cells, and sieve cells), the xylem region (e.g., tracheids and vessels), the bundle sheath layer and/or the endodermis are also considered vascular tissue promoters.

Stem Promoters

Promoters that have preferential activity in the pith, cortex, epidermis, and/or in the vascular bundles or vascular layers of the stem are considered stem promoters. Examples of these promoters are YP0356 (SEQ ID NO:67), YP0108 (SEQ ID NO:88), PT0684, PT0565 (SEQ ID NO:84), PT0710 (SEQ ID NO:18), and YP0080 (SEQ ID NO:90). In some cases, the stem promoters can also be induced by stress like drought (e.g., YP0356 and PT0710).

Inducible Promoters

Inducible promoters confer transcription in response to external stimuli such as chemical agents or environmental stimuli. For example, inducible promoters can confer transcription in response to hormones such as giberellic acid or ethylene, or in response to light or drought. Examples of drought-inducible promoters include YP0380 (SEQ ID NO:70), PT0848 (SEQ ID NO:26), YP0381 (SEQ ID NO:71), YP0337 (SEQ ID NO:66), PT0633 (SEQ ID NO:7), YP0374 (SEQ ID NO:68), PT0710 (SEQ ID NO:18), YP0356 (SEQ ID NO:67), YP0385 (SEQ ID NO:73), YP0396 (SEQ ID NO:74), YP0388 (SEQ ID NO:92), YP0384 (SEQ ID NO:72), PT0688 (SEQ ID NO:15), YP0286 (SEQ ID NO:65), YP0377 (SEQ ID NO:69), PD1367 (SEQ ID NO:78), and PD0901 (SEQ ID NO:93). Examples of nitrogen-inducible promoters include PT0863 (SEQ ID NO:27), PT0829 (SEQ ID NO:23), PT0665 (SEQ ID NO:10), and PT0886 (SEQ ID NO:29). Examples of shade-inducible promoters include PR0924 (SEQ ID NO:91) and PT0678 (SEQ ID NO:13).

Basal Promoters

A basal promoter is the minimal sequence necessary for assembly of a transcription complex required for transcription initiation. Basal promoters frequently include a “TATA box” element that may be located between about 15 and about 35 nucleotides upstream from the site of transcription initiation. Basal promoters also may include a “CCAAT box” element (typically the sequence CCAAT) and/or a GGGCG sequence, which can be located between about 40 and about 200 nucleotides, typically about 60 to about 120 nucleotides, upstream from the transcription start site.

Other Promoters

Other classes of promoters include, but are not limited to, shoot-preferential, callus-preferential, trichome cell-preferential, guard cell-preferential such as PT0678 (SEQ ID NO:13), tuber-preferential, parenchyma cell-preferential, and senescence-preferential promoters. Promoters designated YP0086 (SEQ ID NO:36), YP0188 (SEQ ID NO:58), YP0263 (SEQ ID NO:62), PT0758 (SEQ ID NO:22), PT0743 (SEQ ID NO:21), PT0829 (SEQ ID NO:23), YP0119 (SEQ ID NO:49), and YP0096 (SEQ ID NO:39), as described in the above-referenced patent applications, may also be useful.

Other Regulatory Regions

A 5′ untranslated region (UTR) can be included in nucleic acid constructs described herein. A 5′ UTR is transcribed, but is not translated, and lies between the start site of the transcript and the translation initiation codon and may include the +1 nucleotide. A 3′ UTR can be positioned between the translation termination codon and the end of the transcript. UTRs can have particular functions such as increasing mRNA stability or attenuating translation. Examples of 3′ UTRs include, but are not limited to, polyadenylation signals and transcription termination sequences, e.g., a nopaline synthase termination sequence.

It will be understood that more than one regulatory region may be present in a recombinant polynucleotide, e.g., introns, enhancers, upstream activation regions, transcription terminators, and inducible elements. Thus, for example, more than one regulatory region can be operably linked to the sequence of a polynucleotide encoding a regulatory protein.

Regulatory regions, such as promoters for endogenous genes, can be obtained by chemical synthesis or by subcloning from a genomic DNA that includes such a regulatory region. A nucleic acid comprising such a regulatory region can also include flanking sequences that contain restriction enzyme sites that facilitate subsequent manipulation.

Sequences of Interest and Plants and Plant Cells Containing the Same

Plant cells and plants described herein are useful because expression of a sequence of interest can be modulated to achieve a desired amount and/or specificity of expression by selecting an appropriate association of regulatory region and regulatory protein. A sequence of interest operably linked to a regulatory region can encode a polypeptide or can regulate the expression of a polypeptide. A sequence of interest that encodes a polypeptide can encode a plant polypeptide, a non-plant polypeptide, e.g., a mammalian polypeptide, a modified polypeptide, a synthetic polypeptide, or a portion of a polypeptide. A sequence of interest can be endogenous, i.e., unmodified by recombinant DNA technology from the sequence and structural relationships that occur in nature and operably linked to the unmodified regulatory region. Alternatively, a sequence of interest can be an exogenous nucleic acid. In some embodiments, a sequence of interest is transcribed into an anti-sense or interfering RNA molecule.

More than one sequence of interest can be present in a plant, e.g., two, three, four, five, six, seven, eight, nine, or ten sequences of interest can be present in a plant. If such sequences are exogenous nucleic acids, each sequence of interest can be present on the same nucleic acid construct in such embodiments. Alternatively, each exogenous sequence of interest can be present on separate nucleic acid constructs. The regulatory region operably linked to each sequence of interest can be the same or can be different. In addition, one or more nucleotide sequences encoding a regulatory protein can be included on a nucleic acid construct that is the same as or separate from that containing an associated regulatory region(s) operably linked to a sequence(s) of interest. The regulatory region operably linked to each sequence encoding a regulatory protein can be the same or different.

Lignin Biosynthesis Sequences

In certain cases, a sequence of interest can be an endogenous or exogenous sequence associated with lignin biosynthesis. For example, a transgenic plant cell containing a recombinant nucleic acid encoding a regulatory protein can be effective for modulating the amount and/or rate of lignin biosynthesis. Such effects on lignin biosynthesis typically occur via modulation of transcription of one or more endogenous or exogenous sequences of interest operably linked to an associated regulatory region, e.g., endogenous genes involved in lignin biosynthesis, such as native enzymes or regulatory proteins in lignin biosynthesis pathways, or exogenous sequences involved in lignin biosynthesis pathways introduced via a recombinant nucleic acid construct into a plant cell.

In some embodiments, the coding sequence can encode a polypeptide involved in lignin biosynthesis, e.g., an enzyme or a regulatory protein (such as a transcription factor) involved in lignin biosynthesis described herein. Other components that may be present in a sequence of interest include introns, enhancers, upstream activation regions, and inducible elements.

A suitable sequence of interest can encode an enzyme involved in lignin biosynthesis, such as 4-(hydroxy)cinnamoyl CoA ligase (4CL; EC 6.2.1.12), p-coumarate 3-hydroxylase (C3H), cinnamate 4-hydroxylase (C4H; EC 1.14.13.11), cinnamyl alcohol dehydrogenase (CAD; EC 1.1.1.195), caffeoyl CoA O-methyltransferase (CCoAOMT; EC 2.1.1.104), cinnamoyl CoA reductase (CCR; EC 1.2.1.44), caffeic acid/5-hydroxyferulic acid O-methyltransferase (COMT; EC 2.1.1.68), hydroxycinnamoyl CoA:quinate hydroxycinnamoyltransferase (CQT; EC 2.3.1.99), hydroxycinnamoyl CoA:shikimate hydroxycinnamoyltransferase (CST; EC 2.3.1.133), ferulate 5-hydroxylase (F5H), phenylalanine ammonia-lyase (PAL; EC 4.3.1.5), p-coumaryl CoA 3-hydroxylase (pCCoA3H), or sinapyl alcohol dehydrogenase (SAD).

In some embodiments, a suitable sequence of interest can encode an enzyme involved in polymerization of lignin monomers to form lignin, such as a peroxidase (EC 1.11.1.x) or a laccase (EC 1.10.3.2) enzyme. In some cases, a suitable sequence of interest can encode an enzyme involved in glycosylation of lignin monomers, such as a coniferyl-alcohol glucosyltransferase (EC 2.4.1.111) enzyme, or an enzyme involved in regenerating a monolignol from a monolignol glucoside, such as a coniferin β-glucosidase (EC 3.2.1.126) enzyme. As mentioned above, such a suitable sequence of interest can be transcribed into an anti-sense or interfering RNA molecule.

Phenylpropanoid Sequences of Interest

In some embodiments, a sequence of interest can encode an enzyme involved in flavonoid biosynthesis, such as naringenin-chalcone synthase (EC 2.3.1.74), polyketide reductase, chalcone isomerase (EC 5.5.1.6), flavanone 4-reductase (EC 1.1.1.234), dihydrokaempferol 4-reductase (EC 1.1.1.219), flavone synthase (EC 1.14.11.22), flavone 7-O-beta-glucosyltransferase (EC 2.4.1.81), flavone apiosyltransferase (EC 2.4.2.25), isoflavone-7-O-beta-glucoside 6″-O-malonyltransferase (EC 2.3.1.115), apigenin 4′-O-methyltransferase (EC 2.1.1.75), flavonoid 3′-monooxygenase (EC 1.14.13.21), luteolin O-methyltransferase (EC 2.1.1.42), flavonoid 3′,5′-hydroxylase (EC 1.14.13.88), 4′-methoxyisoflavone 2′-hydroxylase (EC 1.14.13.53), isoflavone 4′-O-methyltransferase (EC 2.1.1.46), flavanone 3-dioxygenase (EC 1.14.11.9), leucocyanidin oxygenase (EC 1.14.11.19), flavonol synthase (EC 1.14.11.23), 2′-hydroxyisoflavone reductase (EC 1.3.1.45), leucoanthocyanidin reductase (EC 1.17.1.3), anthocyanidin reductase (EC 1.3.1.77), flavonol 3-O-glucosyltransferase (EC 2.4.1.91), quercetin 3-O-methyltransferase (EC 2.1.1.76), anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115), flavonol-3-O-glucoside L-rhamnosyltransferase (EC 2.4.1.159), UDP-glucose:anthocyanin 5-O-glucosyltransferase (2.4.1.-), or anthocyanin acyltransferase (2.3.1.-).

In some embodiments, a sequence of interest can encode an enzyme involved in stilbene synthesis such as trihydroxystilbene synthase (EC 2.3.1.95) or an oxidoreductase (EC 1.14.-.-).

In some embodiments, a sequence of interest can encode an enzyme involved in coumarin synthesis such as trans-cinnamate 2-monooxygenase (EC 1.14.13.14), 2-coumarate O-beta-glucosyltransferase (EC 2.4.1.114), a cis-trans-isomerase (EC 5.2.1.-), or a beta-glucosidase (EC 3.2.1.21).

Other Sequences of Interest

Other sequences of interest can encode a therapeutic polypeptide for use with mammals such as humans, e.g., as set forth in Table 1. In certain cases, a sequence of interest can encode an antibody or antibody fragment. An antibody or antibody fragment includes a humanized or chimeric antibody, a single chain Fv antibody fragment, an Fab fragment, and an F(ab)₂ fragment. A chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a mouse monoclonal antibody and a human immunoglobulin constant region. Antibody fragments that have a specific binding affinity can be generated by known techniques. Such antibody fragments include, but are not limited to F(ab′)₂ fragments that can be produced by pepsin digestion of an antibody molecule and Fab fragments that can be generated by reducing the disulfide bridges of F(ab′)₂ fragments. Single chain Fv antibody fragments are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge (e.g., 15 to 18 amino acids), resulting in a single chain polypeptide. Single chain Fv antibody fragments can be produced through standard techniques, such as those disclosed in U.S. Pat. No. 4,946,778. U.S. Pat. No. 6,303,341 discloses immunoglobulin receptors. U.S. Pat. No. 6,417,429 discloses immunoglobulin heavy- and light-chain polypeptides.

TABLE 1 Human therapeutic proteins Bromelain Humatrope ® Proleukin ® Chymopapain Humulin ® (insulin) Protropin ® Papain ® Infergen ® Recombivax-HB ® Activase ® Interferon-gamma-1a Recormon ® Albutein ® Interleukin-2 Remicade ® (s-TNF-r) Angiotensin II Intron ® ReoPro ® Asparaginase Leukine ® (GM-CSF) Retavase ® (TPA) Avonex ® Nartogastrim ® Roferon-A ® Betaseron ® Neumega ® Pegaspargas BioTropin ® Neupogen ® Prandin ® Cerezyme ® Norditropin ® Procrit ® Enbrel ® (s-TNF-r) Novolin ® (insulin) Filgastrim ® Engerix-B ® Nutropin ® Genotropin ® Epogen ® Oncaspar ® Geref ® Sargramostrim Tripedia ® Trichosanthin TriHIBit ® Venoglobin-S ® (HIG)

A sequence of interest can encode a polypeptide or result in a transcription product anti-sense molecule that confers insect resistance, bacterial disease resistance, fungal disease resistance, viral disease resistance, nematode disease resistance, herbicide resistance, enhanced grain composition or quality, enhanced nutrient composition, nutrient transporter functions, enhanced nutrient utilization, enhanced environmental stress tolerance, reduced mycotoxin contamination, female sterility, a selectable marker phenotype, a screenable marker phenotype, a negative selectable marker phenotype, or altered plant agronomic characteristics. Specific examples include, without limitation, a chitinase coding sequence and a glucan endo-1,3-β-glucosidase coding sequence. In some embodiments, a sequence of interest encodes a bacterial ESPS synthase that confers resistance to glyphosate herbicide or a phosphinothricin acetyl transferase coding sequence that confers resistance to phosphinothricin herbicide.

A sequence of interest can encode a polypeptide involved in the production of industrial or pharmaceutical chemicals, modified and specialty oils, enzymes, or renewable non-foods such as fuels and plastics, vaccines and antibodies. U.S. Pat. No. 5,824,779 discloses phytase-protein-pigmenting concentrate derived from green plant juice. U.S. Pat. No. 5,900,525 discloses animal feed compositions containing phytase derived from transgenic alfalfa. U.S. Pat. No. 6,136,320 discloses vaccines produced in transgenic plants. U.S. Pat. No. 6,255,562 discloses insulin. U.S. Pat. No. 5,958,745 discloses the formation of copolymers of 3-hydroxy butyrate and 3-hydroxy valerate. U.S. Pat. No. 5,824,798 discloses starch synthases. U.S. Pat. No. 6,087,558 discloses the production of proteases in plants. U.S. Pat. No. 6,271,016 discloses an anthranilate synthase gene for tryptophan overproduction in plants.

Methods of Inhibiting Expression of a Sequence of Interest

The polynucleotides and recombinant vectors described herein can be used to express or inhibit expression of a gene, such as an endogenous gene involved in lignin biosynthesis, e.g., to alter a lignin biosynthetic pathway in a plant species of interest. The term “expression” refers to the process of converting genetic information of a polynucleotide into RNA through transcription, which is catalyzed by an enzyme, RNA polymerase, and into protein, through translation of mRNA on ribosomes. “Up-regulation” or “activation” refers to regulation that increases the production of expression products (mRNA, polypeptide, or both) relative to basal or native states, while “down-regulation” or “repression” refers to regulation that decreases production of expression products (mRNA, polypeptide, or both) relative to basal or native states.

“Modulated level of gene expression” as used herein refers to a comparison of the level of expression of a transcript of a gene or the amount of its corresponding polypeptide in the presence and absence of a lignin-modulating polypeptide described herein, and refers to a measurable or observable change in the level of expression of a transcript of a gene or the amount of its corresponding polypeptide relative to a control plant or plant cell under the same conditions (e.g., as measured through a suitable assay such as quantitative RT-PCR, a Northern blot, a Western blot, or through an observable change in phenotype, chemical profile, or metabolic profile). A modulated level of gene expression can include up-regulated or down-regulated expression of a transcript of a gene or polypeptide relative to a control plant or plant cell under the same conditions. Modulated expression levels can occur under different environmental or developmental conditions or in different locations than those exhibited by a plant or plant cell in its native state.

A number of nucleic acid based methods, including antisense RNA, ribozyme directed RNA cleavage, post-transcriptional gene silencing (PTGS), e.g., RNA interference (RNAi), and transcriptional gene silencing (TGS) can be used to inhibit gene expression in plants. Suitable polynucleotides include full-length nucleic acids encoding regulatory proteins or fragments of such full-length nucleic acids. In some embodiments, a complement of the full-length nucleic acid or a fragment thereof can be used. Typically, a fragment is at least 10 nucleotides, e.g., at least 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 35, 40, 50, 80, 100, 200, 500 nucleotides or more. Generally, higher homology can be used to compensate for the use of a shorter sequence.

Antisense technology is one well-known method. In this method, a nucleic acid segment from a gene to be repressed is cloned and operably linked to a regulatory region and a transcription termination sequence so that the antisense strand of RNA is transcribed. The recombinant vector is then transformed into plants, as described below, and the antisense strand of RNA is produced. The nucleic acid segment need not be the entire sequence of the gene to be repressed, but typically will be substantially complementary to at least a portion of the sense strand of the gene to be repressed.

In another method, a nucleic acid can be transcribed into a ribozyme, or catalytic RNA, that affects expression of an mRNA. See, U.S. Pat. No. 6,423,885. Ribozymes can be designed to specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. Heterologous nucleic acids can encode ribozymes designed to cleave particular mRNA transcripts, thus preventing expression of a polypeptide. Hammerhead ribozymes are useful for destroying particular mRNAs, although various ribozymes that cleave mRNA at site-specific recognition sequences can be used. Hammerhead ribozymes cleave mRNAs at locations dictated by flanking regions that form complementary base pairs with the target mRNA. The sole requirement is that the target RNA contain a 5′-UG-3′ nucleotide sequence. The construction and production of hammerhead ribozymes is known in the art. See, for example, U.S. Pat. No. 5,254,678 and WO 02/46449 and references cited therein. Hammerhead ribozyme sequences can be embedded in a stable RNA such as a transfer RNA (tRNA) to increase cleavage efficiency in vivo. Perriman et al., Proc. Natl. Acad. Sci. USA, 92(13):6175-6179 (1995); de Feyter and Gaudron, Methods in Molecular Biology, Vol. 74, Chapter 43, “Expressing Ribozymes in Plants”, Edited by Turner, P. C., Humana Press Inc., Totowa, N.J. RNA endoribonucleases which have been described, such as the one that occurs naturally in Tetrahymena thermophile, can be useful. See, for example, U.S. Pat. Nos. 4,987,071 and 6,423,885.

PTGS, e.g., RNAi, can also be used to inhibit the expression of a gene. For example, a construct can be prepared that includes a sequence that is transcribed into an RNA that can anneal to itself, e.g., a double stranded RNA having a stem-loop structure. In some embodiments, one strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the sense coding sequence of the polypeptide of interest, or a fragment thereof, and that is from about 10 nucleotides to about 2,500 nucleotides in length. For example, the length of the sequence that is similar or identical to the sense coding sequence can be from 10 nucleotides to 500 nucleotides, from 15 nucleotides to 300 nucleotides, from 20 nucleotides to 100 nucleotides, or from 25 nucleotides to 100 nucleotides. The other strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the antisense strand, or a fragment thereof, of the coding sequence of the polypeptide of interest, and can have a length that is shorter, the same as, or longer than the corresponding length of the sense sequence. In some cases, one strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the 3′ or 5′ untranslated region, or a fragment thereof, of the mRNA encoding the polypeptide of interest, and the other strand of the stem portion of the double stranded RNA comprises a sequence that is similar or identical to the sequence that is complementary to the 3′ or 5′ untranslated region, respectively, of the mRNA encoding the polypeptide of interest. In other embodiments, one strand of the stem portion of a double stranded RNA comprises a sequence that is similar or identical to the sequence of an intron, or a fragment thereof, in the pre-mRNA encoding the polypeptide of interest, and the other strand of the stem portion comprises a sequence that is similar or identical to the sequence that is complementary to the sequence of the intron, or a fragment thereof, in the pre-mRNA.

The loop portion of a double stranded RNA can be from 3 nucleotides to 5,000 nucleotides, e.g., from 3 nucleotides to 25 nucleotides, from 15 nucleotides to 1,000 nucleotides, from 20 nucleotides to 500 nucleotides, or from 25 nucleotides to 200 nucleotides. The loop portion of the RNA can include an intron, or a fragment thereof. A double stranded RNA can have zero, one, two, three, four, five, six, seven, eight, nine, ten, or more stem-loop structures.

A construct including a sequence that is operably linked to a regulatory region and a transcription termination sequence, and that is transcribed into an RNA that can form a double stranded RNA, is transformed into plants as described herein. Methods for using RNAi to inhibit the expression of a gene are known to those of skill in the art. See, e.g., U.S. Pat. Nos. 5,034,323; 6,326,527; 6,452,067; 6,573,099; 6,753,139; and 6,777,588. See also WO 97/01952; WO 98/53083; WO 99/32619; WO 98/36083; and U.S. Patent Publications 20030175965, 20030175783, 20040214330, and 20030180945.

Constructs containing regulatory regions operably linked to nucleic acid molecules in sense orientation can also be used to inhibit the expression of a gene. The transcription product can be similar or identical to the sense coding sequence, or a fragment thereof, of a polypeptide of interest. The transcription product can also be unpolyadenylated, lack a 5′ cap structure, or contain an unsplicable intron. Methods of inhibiting gene expression using a full-length cDNA as well as a partial cDNA sequence are known in the art. See, e.g., U.S. Pat. No. 5,231,020.

In some embodiments, a construct containing a nucleic acid having at least one strand that is a template for both sense and antisense sequences that are complementary to each other is used to inhibit the expression of a gene. The sense and antisense sequences can be part of a larger nucleic acid molecule or can be part of separate nucleic acid molecules having sequences that are not complementary. The sense or antisense sequence can be a sequence that is identical or complementary to the full-length sequence, or a fragment thereof, of an mRNA, the 3′ or 5′ untranslated region of an mRNA, or an intron in a pre-mRNA encoding a polypeptide of interest. In some embodiments, the sense or antisense sequence is identical or complementary to a sequence of the regulatory region, or a fragment thereof, that drives transcription of the gene encoding a polypeptide of interest. In each case, the sense sequence is the sequence that is complementary to the antisense sequence.

The sense and antisense sequences can be any length greater than about 12 nucleotides (e.g., 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more nucleotides). For example, an antisense sequence can be 21 or 22 nucleotides in length. Typically, the sense and antisense sequences range in length from about 15 nucleotides to about 30 nucleotides, e.g., from about 18 nucleotides to about 28 nucleotides, or from about 21 nucleotides to about 25 nucleotides.

In some embodiments, an antisense sequence is a sequence complementary to an mRNA sequence encoding a lignin-modulating polypeptide described herein. The sense sequence complementary to the antisense sequence can be a sequence present within the mRNA of a lignin-modulating polypeptide. Typically, sense and antisense sequences are designed to correspond to a 15-30 nucleotide sequence of a target mRNA such that the level of that target mRNA is reduced.

In some embodiments, a construct containing a nucleic acid having at least one strand that is a template for more than one sense sequence (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more sense sequences) can be used to inhibit the expression of a gene. Likewise, a construct containing a nucleic acid having at least one strand that is a template for more than one antisense sequence (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more antisense sequences) can be used to inhibit the expression of a gene. For example, a construct can contain a nucleic acid having at least one strand that is a template for two sense sequences and two antisense sequences. The multiple sense sequences can be identical or different, and the multiple antisense sequences can be identical or different. For example, a construct can have a nucleic acid having one strand that is a template for two identical sense sequences and two identical antisense sequences that are complementary to the two identical sense sequences. Alternatively, an isolated nucleic acid can have one strand that is a template for (1) two identical sense sequences 20 nucleotides in length, (2) one antisense sequence that is complementary to the two identical sense sequences 20 nucleotides in length, (3) a sense sequence 30 nucleotides in length, and (4) three identical antisense sequences that are complementary to the sense sequence 30 nucleotides in length. The constructs provided herein can be designed to have any arrangement of sense and antisense sequences. For example, two identical sense sequences can be followed by two identical antisense sequences or can be positioned between two identical antisense sequences.

A nucleic acid having at least one strand that is a template for one or more sense and/or antisense sequences can be operably linked to a regulatory region to drive transcription of an RNA molecule containing the sense and/or antisense sequence(s). In addition, such a nucleic acid can be operably linked to a transcription terminator sequence, such as the terminator of the nopaline synthase (nos) gene. In some cases, two regulatory regions can direct transcription of two transcripts: one from the top strand, and one from the bottom strand. See, for example, Yan et al., Plant Physiol., 141:1508-1518 (2006). The two regulatory regions can be the same or different. The two transcripts can form double-stranded RNA molecules that induce degradation of the target RNA. In some cases, a nucleic acid can be positioned within a T-DNA or P-DNA such that the left and right T-DNA border sequences, or the left and right border-like sequences of the P-DNA, flank or are on either side of the nucleic acid. The nucleic acid sequence between the two regulatory regions can be from about 15 to about 300 nucleotides in length. In some embodiments, the nucleic acid sequence between the two regulatory regions is from about 15 to about 200 nucleotides in length, from about 15 to about 100 nucleotides in length, from about 15 to about 50 nucleotides in length, from about 18 to about 50 nucleotides in length, from about 18 to about 40 nucleotides in length, from about 18 to about 30 nucleotides in length, or from about 18 to about 25 nucleotides in length.

In some nucleic-acid based methods for inhibition of gene expression in plants, a suitable nucleic acid can be a nucleic acid analog. Nucleic acid analogs can be modified at the base moiety, sugar moiety, or phosphate backbone to improve, for example, stability, hybridization, or solubility of the nucleic acid. Modifications at the base moiety include deoxyuridine for deoxythymidine, and 5-methyl-2′-deoxycytidine and 5-bromo-2′-deoxycytidine for deoxycytidine. Modifications of the sugar moiety include modification of the 2′ hydroxyl of the ribose sugar to form 2′-O-methyl or 2′-O-allyl sugars. The deoxyribose phosphate backbone can be modified to produce morpholino nucleic acids, in which each base moiety is linked to a six-membered morpholino ring, or peptide nucleic acids, in which the deoxyphosphate backbone is replaced by a pseudopeptide backbone and the four bases are retained. See, for example, Summerton and Weller, 1997, Antisense Nucleic Acid Drug Dev., 7:187-195; Hyrup et al., Bioorgan. Med. Chem., 4:5-23 (1996). In addition, the deoxyphosphate backbone can be replaced with, for example, a phosphorothioate or phosphorodithioate backbone, a phosphoroamidite, or an alkyl phosphotriester backbone.

Transgenic Plant Cells and Plants

Provided herein are transgenic plant cells and plants comprising at least one recombinant nucleic acid construct or exogenous nucleic acid. A recombinant nucleic acid construct or exogenous nucleic acid can include a regulatory region as described herein, a nucleic acid encoding a regulatory protein as described herein, or both. In certain cases, a transgenic plant cell or plant comprises at least two recombinant nucleic acid constructs or exogenous nucleic acids, one including a regulatory region, and one including a nucleic acid encoding the associated regulatory protein.

A plant or plant cell used in methods of the invention contains a recombinant nucleic acid construct as described herein. A plant or plant cell can be transformed by having a construct integrated into its genome, i.e., can be stably transformed. Stably transformed cells typically retain the introduced nucleic acid with each cell division. A plant or plant cell can also be transiently transformed such that the construct is not integrated into its genome. Transiently transformed cells typically lose all or some portion of the introduced nucleic acid construct with each cell division such that the introduced nucleic acid cannot be detected in daughter cells after a sufficient number of cell divisions. Both transiently transformed and stably transformed transgenic plants and plant cells can be useful in the methods described herein.

Typically, transgenic plant cells used in methods described herein constitute part or all of a whole plant. Such plants can be grown in a manner suitable for the species under consideration, either in a growth chamber, a greenhouse, or in a field. Transgenic plants can be bred as desired for a particular purpose, e.g., to introduce a recombinant nucleic acid into other lines, to transfer a recombinant nucleic acid to other species or for further selection of other desirable traits. Alternatively, transgenic plants can be propagated vegetatively for those species amenable to such techniques. As used herein, a transgenic plant also refers to progeny of an initial transgenic plant provided the progeny inherits the transgene. Progeny includes descendants of a particular plant or plant line. Progeny of an instant plant include seeds formed on F₁, F₂, F₃, F₄, F₅, F₆ and subsequent generation plants, or seeds formed on BC₁, BC₂, BC₃, and subsequent generation plants, or seeds formed on F₁BC₁, F₁BC₂, F₁BC₃, and subsequent generation plants. Seeds produced by a transgenic plant can be grown and then selfed (or outcrossed and selfed) to obtain seeds homozygous for the nucleic acid construct.

Transgenic plant cells growing in suspension culture, or tissue or organ culture, can be useful for extraction of polypeptides or compounds of interest, e.g., polypeptides encoded by sequences of interest, lignin, compounds in a lignin biosynthesis pathway, or flavonoids. For the purposes of this invention, solid and/or liquid tissue culture techniques can be used. When using solid medium, transgenic plant cells can be placed directly onto the medium or can be placed onto a filter film that is then placed in contact with the medium. When using liquid medium, transgenic plant cells can be placed onto a floatation device, e.g., a porous membrane that contacts the liquid medium. Solid medium typically is made from liquid medium by adding agar. For example, a solid medium can be Murashige and Skoog (MS) medium containing agar and a suitable concentration of an auxin, e.g., 2,4-dichlorophenoxyacetic acid (2,4-D), and a suitable concentration of a cytokinin, e.g., kinetin.

When transiently transformed plant cells are used, a reporter sequence encoding a reporter polypeptide having a reporter activity can be included in the transformation procedure and an assay for reporter activity or expression can be performed at a suitable time after transformation. A suitable time for conducting the assay typically is about 1-21 days after transformation, e.g., about 1-14 days, about 1-7 days, or about 1-3 days. The use of transient assays is particularly convenient for rapid analysis in different species, or to confirm expression of a heterologous regulatory protein whose expression has not previously been confirmed in particular recipient cells.

Techniques for introducing nucleic acids into monocotyledonous and dicotyledonous plants are known in the art, and include, without limitation, Agrobacterium-mediated transformation, viral vector-mediated transformation, electroporation and particle gun transformation, e.g., U.S. Pats. 5,538,880, 5,204,253, 6,329,571 and 6,013,863. If a cell or tissue culture is used as the recipient tissue for transformation, plants can be regenerated from transformed cultures if desired, by techniques known to those skilled in the art. See, e.g., Niu et al., Plant Cell Rep. V19:304-310 (2000); Chang and Yang, Bot. Bull. Acad. Sin., V37:35-40 (1996), and Han et al., Biotechnology in Agriculture and Forestry, V44:291 (ed. by Y. P. S. Bajaj), Springer-Verlag, (1999).

A population of transgenic plants can be screened and/or selected for those members of the population that have a desired trait or phenotype conferred by expression of the transgene. For example, a population of progeny of a single transformation event can be screened for those plants having a desired level of expression of a regulatory protein or nucleic acid encoding a regulatory protein. Physical and biochemical methods can be used to identify expression levels. These include Southern analysis or PCR amplification for detection of a polynucleotide; Northern blots, S1 RNase protection, primer-extension, or RT-PCR amplification for detecting RNA transcripts; enzymatic assays for detecting enzyme or ribozyme activity of polypeptides and polynucleotides; and protein gel electrophoresis, Western blots, immunoprecipitation, and enzyme-linked immunoassays to detect polypeptides. Other techniques such as in situ hybridization, enzyme staining, and immunostaining also can be used to detect the presence or expression of polypeptides and/or polynucleotides. Methods for performing all of the referenced techniques are known. As an alternative, a population of plants comprising independent transformation events can be screened for those plants having a desired trait, such as a modulated lignin content. Selection and/or screening can be carried out over one or more generations, which can be useful to identify those plants that have a desired trait, such as an increased lignin content. Selection and/or screening can also be carried out in more than one geographic location. In some cases, transgenic plants can be grown and selected under conditions which induce a desired phenotype or are otherwise necessary to produce a desired phenotype in a transgenic plant. In addition, selection and/or screening can be carried out during a particular developmental stage in which the phenotype is exhibited by the plant. Selection and/or screening can be carried out to choose those transgenic plants having a statistically significant difference in lignin content relative to a control plant that lacks the transgene. Selected or screened transgenic plants have an altered phenotype as compared to a corresponding control plant, as described in the “Transgenic Plant Phenotypes” section herein.

Plant Species

The polynucleotides and vectors described herein can be used to transform a number of monocotyledonous and dicotyledonous plants and plant cell systems, including dicots such as alfalfa, almond, amaranth, apple, apricot, ash, avocado, beans (including kidney beans, lima beans, dry beans, green beans), beech, bilberry, birch, black-eyed pea, blackberry, blessed milk thistle, blueberry, brazil nut, broccoli, Brussels sprouts, buckwheat, cabbage, canola, carrot, cashew, castor bean, celery, chamomile, cherry, chick peas, chicory, chocolate, clover, cocoa, coffee, cotton, cottonseed, crambe, eucalyptus, flax, foxglove, gooseberry, grape, grapefruit, hawthorn, hazelnut, hemp, jatropha, jojoba, lemon, lentils, lettuce, linseed, loganberry, lupine, macadamia nut, mahogany, mango, maple, melon (e.g., watermelon, cantaloupe), mustard, neem, oak, olive, orange, parsley, peach, peanut, peach, pear, peas, pecan, pepper, pistachio, plum, poplar, poppy, potato, pumpkin, oilseed rape, quinoa, rapeseed (high erucic acid and canola), raspberry, red clover, rhubarb, safflower, sesame, soaptree bark, soybean, spinach, strawberry, sugar beet, sunflower, sweet potatoes, tangerine, tea, teak, tomato, vetch, walnut, willow, and yams, as well as monocots such as banana, barley, bluegrass, chives, coconut, corn, date palm, fescue, field corn, garlic, ginger, millet, miscanthus, oat, oil palm, onion, palm kernel oil, pineapple, popcorn, rice, rye, ryegrass, sorghum, sudangrass, sugarcane, sweet corn, switchgrass, turf grasses, timothy, and wheat. Gymnosperms such as fir, pine, and spruce can also be suitable.

Thus, the methods and compositions described herein can be used with dicotyledonous plants belonging, for example, to the orders Apiales, Arecales, Aristolochiales, Asterales, Batales, Campanulales, Capparales, Caryophyllales, Casuarinales, Celastrales, Cornales, Cucurbitales, Diapensales, Dilleniales, Dipsacales, Ebenales, Ericales, Eucomiales, Euphorbiales, Fabales, Fagales, Gentianales, Geraniales, Haloragales, Hamamelidales, Illiciales, Juglandales, Lamiales, Laurales, Lecythidales, Leitneriales, Linales, Magniolales, Malpighiales, Malvales, Myricales, Myrtales, Nymphaeales, Papaverales, Piperales, Plantaginales, Plumbaginales, Podostemales, Polemoniales, Polygalales, Polygonales, Primulales, Proteales, Rafflesiales, Ranunculales, Rhamnales, Rosales, Rubiales, Salicales, Santales, Sapindales, Sarraceniaceae, Scrophulariales, Solanales, Trochodendrales, Theales, Umbellales, Urticales, and Violates. The methods and compositions described herein also can be utilized with monocotyledonous plants such as those belonging to the orders Alismatales, Arales, Arecales, Asparagales, Bromeliales, Commelinales, Cyclanthales, Cyperales, Eriocaulales, Hydrocharitales, Juncales, Liliales, Najadales, Orchidales, Pandanales, Poales, Restionales, Triuridales, Typhales, Zingiberales, and with plants belonging to Gymnospermae, e.g., Cycadales, Ephedrales, Ginkgoales, Gnetales, Taxales, and Pinales.

The methods and compositions can be used over a broad range of plant species, including species from the dicot genera Abelmoschus, Acokanthera, Acer, Aconitum, Aesculus, Afzelia, Alangium, Alchornea, Alexa, Alnus, Alseodaphne, Amaranthus, Ammodendron, Anabasis, Anacardium, Andrographis, Angophora, Anisodus, Anthemis, Apium, Apocynum, Arabidopsis, Arachis, Argemone, Artemisia, Asclepias, Atropa, Azadirachta, Beilschmiedia, Berberis, Bertholletia, Beta, Betula, Bixa, Bleekeria, Borago, Brassica, Calendula, Camellia, Camptotheca, Canarium, Cannabis, Capsicum, Carthamus, Carya, Catharanthus, Centella, Cephaelis, Chelidonium, Chenopodium, Chrysanthemum, Cicer, Cichorium, Cinchona, Cinnamomum, Cissampelos, Citrus, Citrullus, Cocculus, Cocos, Coffea, Cola, Coleus, Convolvulus, Coptis, Corylus, Corymbia, Crambe, Crataegus, Crotalaria, Croton, Cucumis, Cucurbita, Cuphea, Cytisus, Datura, Daucus, Dendromecon, Dianthus, Dichroa, Digitalis, Dioscorea, Duguetia, Eriogonum, Erythroxylum, Eschscholzia, Eucalyptus, Euphorbia, Euphoria, Fagus, Ficus, Fragaria, Fraxinus, Galega, Gelsemium, Glaucium, Glycine, Glycyrrhiza, Gossypium, Helianthus, Heliotropium, Hemsleya, Hevea, Hydrastis, Hyoscyamus, Jatropha, Juglans, Lactuca, Landolphia, Lavandula, Lens, Linum, Litsea, Lobelia, Luffa, Lupinus, Lycopersicon, Macadamia, Mahonia, Majorana, Malus, Mangifera, Manihot, Meconopsis, Medicago, Menispermum, Mentha, Micropus, Nicotiana, Ocimum, Olea, Origanum, Papaver, Parthenium, Persea, Petroselinum, Petunia, Phaseolus, Physostigma, Pilocarpus, Pistacia, Pisum, Poinsettia, Populus, Prunus, Psychotria, Pyrus, Quercus, Quillaja, Rabdosia, Raphanus, Rauwolfia, Rheum, Rhizocarya, Ribes, Ricinus, Rosa, Rosmarinus, Rubus, Rubia, Salix, Salvia, Sanguinaria, Scopolia, Senecio, Sesamum, Silybum, Simmondsia, Sinapis, Sinomenium, Solanum, Sophora, Spinacia, Stephania, Strophanthus, Strychnos, Tagetes, Tanacetum, Tectona, Theobroma, Thymus, Trifolium, Trigonella, Vaccinium, Vicia, Vigna, Vinca, and Vitis; and the monocot genera Agrostis, Allium, Alopecurus, Alstroemeria, Ananas, Andropogon, Areca, Arundo, Asparagus, Avena, Cocos, Colchicum, Convallaria, Curcuma, Cynodon, Elaeis, Eragrostis, Erianthus, Festuca, Festulolium, Galanthus, Hemerocallis, Hordeum, Lemna, Lolium, Milium, Miscanthus, Musa, Oryza, Panicum, Pennisetum, Phalaris, Phleum, Phoenix, Poa, Ruscus, Saccharum, Secale, Sorghum, Spartina, Triticosecale, Triticum, Uniola, Veratrum, Zea, Zingiber, and Zoysia; and the gymnosperm genera Abies, Cephalotaxus, Cunninghamia, Ephedra, Picea, Pinus, Pseudotsuga and Taxus.

In some embodiments, a plant is a member of the species Abelmoschus esculentus (okra), Abies spp. (fir), Acer spp. (maple), Allium cepa (onion), Alstroemeria spp., Ananas comosus (pineapple), Andrographis paniculata, Andropogon gerardii (big bluestem), Artemisia annua, Arundo donax (giant reed), Atropa belladonna, Avena sativa, bamboo, bentgrass (Agrostis spp.), Berberis spp., Beta vulgaris (sugarbeet), Bixa orellana, Brassica juncea, Brassica napus (canola), Brassica rapa, Brassica oleracea (broccoli, cauliflower, brusselsprouts), Calendula officinalis, Camellia sinensis (tea), Camptotheca acuminate, Cannabis sativa, Capsicum annum (hot & sweet pepper), Carthamus tinctorius (safflower), Catharanthus roseus, Cephalotaxus spp., Chrysanthemum parthenium, Cinchona officinalis, Citrullus lanatus (watermelon), Coffea arabica (coffee), Colchicum autumnale, Coleus forskohlii, Cucumis melo (melon), Cucumis sativus (cucumber), Cucurbita maxima (squash), Cucurbita moschata (squash), Cynodon dactylon (bermudagrass), Datura stomonium, Dianthus caryophyllus (carnation), Digitalis lanata, Digitalis purpurea, Dioscorea spp., Elaeis guineensis (palm), Ephedra sinica, Ephedra spp., Erianthus spp., Erythroxylum coca, Eucalyptus spp. (eucalyptus), Festuca arundinacea (tall fescue), Fragaria ananassa (strawberry), Galanthus wornorii, Glycine max (soybean), Gossypium hirsutum (cotton), Gossypium herbaceum, Helianthus annuus (sunflower), Hevea spp. (rubber), Hordeum vulgare, Hyoscyamus spp., Jatropha curcas (jatropha), Lactuca sativa (lettuce), Linum usitatissimum (flax), Lupinus albus (lupin), Lycopersicon esculentum (tomato), Lycopodium serratum (=Huperzia serrata), Lycopodium spp., Manihot esculenta (cassava), Medicago sativa (alfalfa), Mentha piperita (mint), Mentha spicata (mint), Miscanthus giganteus (miscanthus), Miscanthus hybrid (Miscanthus×giganteus), Miscanthus sinensis, Miscanthus sacchariflorus, Musa paradisiaca (banana), Nicotiana tabacum (tobacco), Oryza sativa (rice), Panicum spp., Panicum virgatum (switchgrass), Papaver somniferum (opium poppy), Papaver orientate, Parthenium argentatum (guayule), Pennisetum glaucum (pearl millet), Pennisetum purpureum (elephant grass), Petunia spp. (petunia), Phalaris arundinacea (reed canarygrass), Pinus spp. (pine), Poinsettia pulcherrima (poinsettia), Populus spp., Populus trichocarpa (poplar), Populus tremuloides (aspen), Rauwolfia serpentina, Rauwolfia spp., Ricinus communis (castor), Rosa spp. (rose), Saccharum spp. (energycane), Saccharum officinarum Salix spp. (willow), Sanguinaria canadensis, Scopolia spp., Secale cereale (rye), Solanum melongena (eggplant), Solanum tuberosum (potato), Sorghum spp., Sorghum almum, Sorghum bicolor (sorghum), Sorghum halapense, Sorghum vulgare, Spartina pectinata (prairie cordgrass), Spinacea oleracea (spinach), Tanacetum parthenium, Taxus baccata, Taxus brevifolia, Theobroma cacao (cocoa), Triticale (wheat X rye), Triticum aestivum (wheat), Uniola paniculata (oats), Veratrum californica, Vinca rosea, Vitis vinifera (grape), and Zea mays (corn).

In certain embodiments, the polynucleotides and vectors described herein can be used to transform a number of monocotyledonous and dicotyledonous plants and plant cell systems, wherein such plants are hybrids of different species or varieties of a specific (e.g., Saccharum sp.×Miscanthus sp.)

Transgenic Plant Phenotypes

Compositions and methods described herein are useful for modulating the amount and/or chemical composition of lignin in plants. For example, the regulatory proteins described herein can modulate transcription of sequences involved in lignin biosynthesis. Thus, a transgenic plant, tissue, or cell comprising a recombinant nucleic acid expressing such a regulatory protein can have a modulated amount and/or rate of lignin biosynthesis when the plant contains an associated regulatory region, either as a genomic sequence or introduced in a recombinant nucleic acid construct. Plants, tissues, or cells containing a recombinant nucleic acid construct described herein typically have a difference in the amount and/or rate of synthesis of lignin, relative to a corresponding control plant, tissue, or cell that is not transformed with the recombinant nucleic acid construct.

A number of different types of lignin, based on chemical and structural features, can be produced by different species of plants, by different tissues of the same plant, or by different parts of the same plant cell. Such lignins include, without limitation, lignins comprising primarily or only coniferyl alcohols such as guaiacyl lignin, lignins comprising primarily or only sinapyl alcohols such as syringyl lignin, lignins comprising primarily or only p-coumaryl alcohols such as p-hydroxyphenyl lignin, and lignins comprising primarily or only coniferyl and sinapyl alcohols such as guaiacyl-syringyl lignin. In addition, other compounds can be incorporated into lignins, including, without limitation, coniferyl/sinapyl p-coumarate, coniferyl/sinapyl p-hydroxybenzoate, coniferyl/sinapyl acetate, ferulate esters, 5-hydroxy-coniferyl alcohol, 3,4-dihydroxy-cinnamyl alcohol, feruloyl amides such as tyramine ferulate, coniferaldehyde/sinapaldehyde, vanillin/syringaldehyde, benzodioxanes, 5-hydroxyguaiacyl, and dihydroconiferyl/dihydro-p-coumaryl alcohol.

The amount and/or rate of synthesis of any type of lignin can be modulated, e.g., increased or decreased, in a transgenic plant, tissue, or cell relative to a control plant, tissue, or cell using the methods described herein. In some cases, the amounts of two or more types of lignin (e.g., two, three, four, five, six, seven, eight, nine, ten or even more types of lignin) can be independently modulated relative to a control plant, tissue, or cell.

In some embodiments, the amount of lignin is decreased in transgenic plants, tissues, or cells described herein (e.g., transgenic plants expressing a regulatory protein or an antisense or double-stranded RNA targeted to a regulatory protein as described herein). A decrease ratio can be expressed as the ratio of the lignin in such a transgenic plant, tissue, or cell on a weight basis (e.g., fresh weight basis) as compared to the lignin in a corresponding control plant, tissue, or cell (e.g., a corresponding plant, tissue, or cell that lacks the recombinant nucleic acid encoding the regulatory protein or the antisense or double-stranded RNA targeted to a regulatory protein). The decrease ratio can be from about 0.05 to about 0.90. In certain cases, the ratio can be from about 0.2 to about 0.6, or from about 0.4 to about 0.6, or from about 0.3 to about 0.5, or from about 0.2 to about 0.4.

In some cases, a decrease in the amount of lignin in a transgenic plant described herein can be calculated as a percent decrease in the weight of lignin extracted per weight of tissue of the transgenic plant relative to the weight of lignin extracted per weight of tissue of a corresponding control plant. For example, the amount of lignin in a tissue of a transgenic plant provided herein can be decreased by about 1% to about 10%, or about 5% to about 15%, or about 20% to about 50%, or about 25% to about 40%, or about 30% to about 60%, or about 50% to about 75%, or about 75% to about 90% relative to the amount of lignin in a tissue of a corresponding control plant.

The decrease in amount of lignin can be restricted in some embodiments to particular tissues and/or organs, relative to other tissues and/or organs. For example, a transgenic plant can have a decreased amount of lignin in stem tissue relative to leaf tissue. The decreased amount of lignin can be in the cell wall of plant cells such as tracheids, xylem fibres, and sclereids.

An increase in the amount of lignin in a transgenic plant, tissue, or cell described herein can be from about 1.02-fold to about 10-fold, about 1.03-fold to about 1.7-fold, or about 1.04-fold to about 1.6-fold, or about 1.05-fold to about 1.7-fold, or about 1.06-fold to about 2.3-fold, or about 1.07-fold to about 2.5-fold, or about 1.08-fold to about 2-fold, or about 1.09-fold to about 2.4-fold, or about 1.1-fold to about 2-fold, or about 1.2-fold to about 3-fold, or about 1.3-fold to about 2.5-fold, or about 1.4-fold to about 3-fold, or about 1.5-fold to about 5-fold, or about 2-fold to about 6-fold, or about 2-fold to about 5-fold, or about 1.5-fold to 7-fold, or about 3-fold to about 4-fold, or about 3-fold to about 7.5-fold, or about 4-fold to about 8-fold, or about 5-fold to about 10-fold higher than the amount in corresponding control plants, tissues, or cells.

In some cases, an increase in the amount of lignin in a transgenic plant described herein can be calculated as a percent increase in the weight of lignin extracted per weight of tissue of the transgenic plant relative to the weight of lignin extracted per weight of tissue of a corresponding control plant. For example, the amount of lignin in a tissue of a transgenic plant provided herein can be increased by about 1% to about 10%, or about 5% to about 15%, or about 20% to about 50%, or about 25% to about 40%, or about 30% to about 60%, or about 50% to about 75%, or about 75% to about 100%, or about 90% to about 150%, or about 50% to about 200%, or about 100% to about 300%, or about 150% to about 500%, or about 200 to about 600%, or about 300% to about 800% relative to the amount of lignin in a tissue of a corresponding control plant.

In some embodiments, the lignin that is increased in a tissue of a transgenic plant described herein is either not produced or is not detectable in a corresponding tissue of a control plant. Thus, in such embodiments, the increase in lignin is infinitely high. For example, in certain cases, a regulatory protein described herein may activate a biosynthetic pathway in a plant tissue that is not normally activated or operational in a control plant tissue and one or more new types of lignin that were not previously produced in that plant tissue can be produced.

The increase in amount of lignin can be restricted in some embodiments to particular tissues and/or organs, relative to other tissues and/or organs. For example, a transgenic plant can have an increased amount of lignin in stem tissue relative to leaf tissue. The increased amount of lignin can be in the cell wall of plant cells such as tracheids, xylem fibres, and sclereids.

In some embodiments, the amount of lignin in transgenic switchgrass (Panicum virgatum) expressing a regulatory protein or an antisense or double-stranded RNA targeted to a regulatory protein as described herein can be decreased by about 40% to about 75%, or about 45% to about 70%, or about 48% to about 68%, or about 50% to about 66%, or about 53% to about 66%, or about 55% to about 65%, or about 57% to about 71%, or about 50% to about 70%, or about 55% to about 60%, or about 60% to about 65% by weight relative to the amount of lignin in corresponding control switchgrass (e.g., corresponding wild-type switchgrass or switchgrass that lacks the nucleic acid encoding the regulatory protein or the antisense or double-stranded RNA targeted to a regulatory protein). In some cases, the decrease ratio of lignin in transgenic switchgrass as compared to the lignin in corresponding control switchgrass can be from about 0.4 to about 0.8, or about 0.4 to about 0.7, or about 0.45 to about 0.7, or about 0.5 to about 0.66, or about 0.5 to about 0.7, or about 0.5 to about 0.68, or about 0.55 to about 0.7, or about 0.6 to about 0.7, or about 0.53 to about 0.66.

In some embodiments, the amount of lignin in transgenic switchgrass expressing a regulatory protein or an antisense or double-stranded RNA targeted to a regulatory protein as described herein can be increased by about 100% to about 300%, or about 100% to about 275%, or about 125% to about 300%, or about 125% to about 275%, or about 150% to about 275%, or about 150% to about 250%, or about 175% to about 250%, or about 175% to about 225%, or about 100% to about 250%, or about 150% to 300% by weight as compared to the amount of lignin in corresponding control switchgrass. In some cases, an increase in lignin in transgenic switchgrass described herein can be from about 1.2-fold to about 3-fold, or about 1.3-fold to about 2-fold, or about 1.3-fold to about 2.5-fold, or about 1.5-fold to about 2.1-fold, or about 1.25-fold to about 2.75-fold, or about 1.2-fold to about 2.15-fold, or about 1.4-fold to about 2.8-fold, or about 1.5-fold to about 2.5-fold, or about 1.75-fold to about 2.75-fold, or about 1.2-fold to about 1.9-fold relative to corresponding control switchgrass.

The amount of lignin in a plant can be determined by known techniques, e.g., the acid detergent, Klason, acetyl bromide, and permanganate lignin methods. See, for example, Hatfield and Fukushima, Crop Sci., 45:832-839 (2005); and Methods in Lignin Chemistry, Dence and Lin, eds., Springer-Verlag, Berlin, p. 33-61 (1992). Pyrolysis-gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry (LC-MS), or a degradative method, e.g., the DFRC method or thioacidolysis, combined with mass spectrometry also can be used. If desired, the composition and structure of lignin can be characterized by GC-MS, LC-MS, nuclear magnetic resonance spectroscopy, Fourier-transform infrared spectroscopy, and/or other known techniques. In addition, histochemical analysis can be performed to determine the amount and distribution of lignin in a plant. For example, tissue sections can be stained with toluidine blue O (TBO), the Wiesner reagent, or the Maule reagent. TBO is a metachromatic stain that imparts a turquoise color to lignified cell walls and stains non-lignified cell walls purple. Phloroglucinol stains lignified cells red upon reaction with hydroxycinnamaldehyde groups present in the polymer. The Maule reagent is a histochemical stain that allows syringyl lignin to be distinguished chromogenically from guaiacyl lignin in situ. A pink or red color can indicate the presence of syringyl units, whereas a light to dark brown color can indicate the presence of guaiacyl units.

A transgenic plant, tissue, or cell expressing a regulatory protein described herein can have a modulated, e.g., increased or decreased, level of one or more compounds in a lignin biosynthesis pathway as compared to a control plant, tissue, or cell not transgenic for the particular regulatory protein. In certain cases, the amount of more than one compound (e.g., two, three, four, five, six, seven, eight, nine, ten or even more compounds) included in a lignin biosynthetic pathway can be modulated relative to a control plant, tissue, or cell that is not transgenic for a regulatory protein described herein. Such a compound can be, for example, a precursor compound, an intermediate compound, or an end product in a lignin biosynthesis pathway.

Compounds in a lignin biosynthesis pathway include, without limitation, phenylalanine, cinnamic acid, p-coumaric acid, p-coumaraldehyde, p-coumaryl alcohol, caffeic acid, ferulic acid, 5-hydroxy-ferulic acid, 5-hydroxy-feruloyl CoA, sinapic acid, sinapoyl CoA, p-coumaroyl CoA, p-coumaroyl shikimic acid, p-coumaroyl quinic acid, caffeoyl shikimic acid, caffeoyl quinic acid, caffeoyl CoA, feruloyl CoA, coniferaldehyde, 5-hydroxy-coniferaldehyde, sinapaldehyde, coniferyl alcohol, 5-hydroxy-coniferyl alcohol, sinapyl alcohol, caffeyl aldehyde, and caffeyl alcohol.

The amount of one or more compounds in a lignin biosynthesis pathway can be increased or decreased in transgenic cells or tissues expressing a regulatory protein described herein. An increase can be from about 1.2-fold to about 150-fold, about 1.3-fold to about 20-fold, or about 1.2-fold to about 3-fold, or about 1.3-fold to about 2-fold, or about 1.4-fold to about 3-fold, or about 2-fold to about 4-fold, or about 2-fold to about 5-fold, or about 1.5-fold to 7-fold, or about 3-fold to about 4-fold, or about 3-fold to about 7-fold, or about 4-fold to about 8-fold, or about 5-fold to about 10-fold, or about 10-fold to about 15-fold, or about 12-fold to about 18-fold, or about 14-fold to about 22-fold, or about 18-fold to about 30-fold, or about 10-fold to about 100-fold, or about 30-fold to about 100-fold, or about 75-fold to about 130-fold, or about 5-fold to about 50-fold, or about 40-fold to about 150-fold higher than the amount in corresponding control cells or tissues that lack the recombinant nucleic acid encoding the regulatory protein.

In some embodiments, the compound in a lignin biosynthesis pathway that is increased in transgenic cells expressing a regulatory protein described herein is either not produced or is not detectable in a corresponding control cell that lacks the recombinant nucleic acid encoding the regulatory protein. Thus, in such embodiments, the increase in such a compound is infinitely high as compared to corresponding control cells or tissues that lack the recombinant nucleic acid encoding the regulatory protein. For example, in certain cases, a regulatory protein described herein may activate a biosynthetic pathway in a plant that is not normally activated or operational in a control plant, and one or more compounds in a lignin biosynthetic pathway that were not previously produced in that plant species can be produced.

The increase in amount of one or more compounds in a lignin biosynthesis pathway can be restricted in some embodiments to particular tissues and/or organs, relative to other tissues and/or organs. For example, a transgenic plant can have an increased amount of a lignin biosynthesis compound in stem tissue relative to leaf or root tissue.

In some embodiments, the amount of one or more than one compound in a lignin biosynthesis pathway is decreased in transgenic cells expressing a regulatory protein as described herein. A decrease ratio can be expressed as the ratio of the compound in such a transgenic cell on a weight basis (e.g., fresh weight basis) as compared to the compound in a corresponding control cell that lacks the recombinant nucleic acid encoding the regulatory protein. The decrease ratio can be from about 0.05 to about 0.90. In certain cases, the ratio can be from about 0.2 to about 0.6, or from about 0.4 to about 0.6, or from about 0.3 to about 0.5, or from about 0.2 to about 0.4.

In certain embodiments, the compound in a lignin biosynthesis pathway that is decreased in transgenic cells expressing a regulatory protein as described herein is decreased to an undetectable level as compared to the level in corresponding control cells that lack the recombinant nucleic acid encoding the regulatory protein. Thus, in such embodiments, the decrease ratio for such a compound is zero.

The decrease in amount of one or more compounds in a lignin biosynthesis pathway can be restricted in some embodiments to particular tissues and/or organs, relative to other tissues and/or organs. For example, a transgenic plant can have a decreased amount of a compound in stem tissue relative to leaf tissue.

In some embodiments, the amounts of two or more compounds in a lignin biosynthesis pathway are increased and/or decreased, e.g., the amounts of two, three, four, five, six, seven, eight, nine, ten, or more, lignin compounds are independently increased and/or decreased. The amount of a lignin compound can be determined by known techniques, e.g., by extraction of compounds in a lignin biosynthesis pathway from a plant tissue followed by gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS). If desired, the structure of the lignin compound can be confirmed by GC-MS, LC-MS, nuclear magnetic resonance and/or other known techniques.

In addition to having a modulated amount of lignin and/or a modulated level of one or more than one compound in a lignin biosynthesis pathway, a transgenic plant or cell produced using the materials and methods described herein can produce one or more lignins having an altered structure and/or composition relative to the lignin(s) produced by a corresponding control plant or cell that is not transformed with the recombinant nucleic acid construct. For example, the lignin composition can be altered from essentially 100% guaiacyl units to essentially 100% syringyl units. In some cases, the ratio of syringyl to guaiacyl units incorporated into lignin in a transgenic plant can be modulated relative to the corresponding ratio in a control plant. For example, the ratio of syringyl to guaiacyl units can be increased, e.g., by 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2.0-fold, 2.1-fold, 2.2-fold, 2.3-fold, 2.4-fold, 2.5-fold, 2.6-fold, 2.7-fold, 2.8-fold, 2.9-fold, 3.0-fold, or more than 3.0-fold, in a transgenic plant provided herein as compared to the corresponding ratio in a control plant. In some cases, the ratio of syringyl to guaiacyl units incorporated into lignin in a transgenic plant described herein can be decreased, e.g., by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 70%, 80%, 90%, 100%, or more than 100%, as compared to the corresponding ratio in a control plant. In some cases, the composition of lignin can be altered in a transgenic plant by having compounds incorporated into lignin that are not normally incorporated into lignin in a wild-type plant. Such compounds can include, without limitation, dihydroconiferyl alcohol, coniferaldehyde, hydroxycinnamaldehydes, and hydroxybenzaldehydes. The composition of lignin in a plant can be determined using well known methods, such as those described herein.

Methods of Screening for Associations and Modulating Expression of Sequences of Interest

Provided herein are methods of screening for novel regulatory region-regulatory protein association pairs. The described methods can thus determine whether or not a given regulatory protein can activate a given regulatory region (e.g., to modulate expression of a sequence of interest operably linked to the given regulatory region).

A method of determining whether or not a regulatory region is activated by a regulatory protein can include determining whether or not reporter activity is detected in a plant cell transformed with a recombinant nucleic acid construct comprising a test regulatory region operably linked to a nucleic acid encoding a polypeptide having the reporter activity and with a recombinant nucleic acid construct comprising a nucleic acid encoding a regulatory protein described herein. Detection of the reporter activity indicates that the test regulatory region is activated by the regulatory protein. In certain cases, the regulatory region is a regulatory region as described herein, e.g., comprising a nucleic acid sequence having 80% or greater sequence identity to a regulatory region as set forth in SEQ ID NOs:1909-1918.

For example, a plant can be made that is stably transformed with a sequence encoding a reporter operably linked to the regulatory region under investigation. The plant is inoculated with Agrobacterium containing a sequence encoding a regulatory protein on a Ti plasmid vector. A few days after inoculation, the plant tissue is examined for expression of the reporter, or for detection of reporter activity associated with the reporter. If reporter expression or activity is observed, it can be concluded that the regulatory protein increases transcription of the reporter coding sequence, such as by binding the regulatory region. A positive result indicates that expression of the regulatory protein being tested in a plant would be effective for increasing the in planta amount and/or rate of biosynthesis of one or more sequences of interest operably linked to the associated regulatory region.

Similarly, a method of determining whether or not a regulatory region is activated by a regulatory protein can include determining whether or not reporter activity is detected in a plant cell transformed with a recombinant nucleic acid construct comprising a regulatory region as described herein operably linked to a reporter nucleic acid, and with a recombinant nucleic acid construct comprising a nucleic acid encoding a test regulatory protein. Detection of reporter activity indicates that the regulatory region is activated by the test regulatory protein. In certain cases, the regulatory protein is a regulatory protein as described herein, e.g., comprising a polypeptide sequence having 80% or greater sequence identity to a polypeptide sequence set forth in any of SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, or SEQ ID NO:2087.

A transformation can be a transient transformation or a stable transformation, as discussed previously. The regulatory region and the nucleic acid encoding a test regulatory protein can be on the same or different nucleic acid constructs.

A reporter activity, such as an enzymatic or optical activity, can permit the detection of the presence of the reporter polypeptide in situ or in vivo, either directly or indirectly. For example, a reporter polypeptide can itself be bioluminescent upon exposure to light. A reporter polypeptide also can catalyze a chemical reaction in vivo that yields a detectable product that is localized inside or that is associated with a cell that expresses the chimeric polypeptide. Exemplary bioluminescent reporter polypeptides that emit light in the presence of additional polypeptides, substrates or cofactors include firefly luciferase and bacterial luciferase. Bioluminescent reporter polypeptides that fluoresce in the absence of additional proteins, substrates or cofactors when exposed to light having a wavelength in the range of 300 nm to 600 nm include, for example: amFP486, Mut15-amFP486, Mut32-amFP486, CNFP-MODCd1 and CNFP-MODCd2; asFP600, mut1-RNFP, NE-RNFP, d1RNFP and d2RNFP; cFP484, Δ19-cFP484 and Δ38-cFP484; dgFP512; dmFP592; drFP583, E5 drFP583, E8 drFP583, ESUP drFP583, ESdown drFP583, E57 drFP583, AG4 drFP583 and AG4H drFP583; drFP583/dmFP592, drFP583/dmFP592-2G and drFP583/dmFP592-Q3; dsFP483; zFP506, N65M-zFP506, d1zFP506 and d2zFP506; zFP538, M128V-zFP538, YNFPM128V-MODCd1 and YNFPM128V-MODCd2; GFP; EGFP, ECFP, EYFP, EBFP, BFP2; d4EGFP, d2EGFP, and d1EGFP; and DsRed and DsRed1. See WO 00/34318; WO 00/34320; WO 00/34319; WO 00/34321; WO 00/34322; WO 00/34323; WO 00/34324; WO 00/34325; WO 00/34326; GenBank Accession No. AAB57606; Clontech User Manual, April 1999, PT2040-1, version PR94845; Li et al., J Biol Chem 1998, 273:34970-5; U.S. Pat. No. 5,777,079; and Clontech User Manual, October 1999, PT34040-1, version PR9X217. Reporter polypeptides that catalyze a chemical reaction that yields a detectable product include, for example, β-galactosidase or β-glucuronidase. Other reporter enzymatic activities for use in the invention include neomycin phosphotransferase activity and phosphinothricin acetyl transferase activity.

In some cases, it is known that a particular transcription factor can activate transcription from a particular lignin regulatory region(s), e.g., a regulatory region involved in lignin biosynthesis. In these cases, similar methods can also be useful to screen other regulatory regions, such as other regulatory regions involved in lignin biosynthesis, to determine whether they are activated by the same transcription factor. Thus, the method can comprise transforming a plant cell with a nucleic acid comprising a test regulatory region operably linked to a nucleic acid encoding a polypeptide having reporter activity. The plant cell can include a recombinant nucleic acid encoding a regulatory protein operably linked to a regulatory region that drives transcription of the regulatory protein in the cell. If reporter activity is detected, it can be concluded that the regulatory protein activates transcription mediated by the test regulatory region.

Provided herein also are methods to modulate expression of sequences of interest. Modulation of expression can be expression itself, an increase in expression, or a decrease in expression. Such a method can involve transforming a plant cell with, or growing a plant cell comprising, at least one recombinant nucleic acid construct. A recombinant nucleic acid construct can include a regulatory region as described above, e.g., comprising a nucleic acid having 80% or greater sequence identity to a regulatory region set forth in SEQ ID NOs:1909-1918, where the regulatory region is operably linked to a nucleic acid encoding a sequence of interest. In some cases, a recombinant nucleic acid construct can further include a nucleic acid encoding a regulatory protein as described above, e.g., comprising a polypeptide sequence having 80% or greater sequence identity to a polypeptide sequence set forth in any of SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, or SEQ ID NO:2087. In other cases, the nucleic acid encoding the described regulatory protein is contained on a second recombinant nucleic acid construct. In either case, the regulatory region and the regulatory protein are associated, e.g., as indicated in Table 4 (in Example 2) or as described herein (e.g., all orthologs/homologs of a regulatory protein are also considered to associate with the regulatory regions shown to associate with a given regulatory protein in Table 4 (in Example 2). A plant cell is typically grown under conditions effective for expression of the regulatory protein.

As will be recognized by those having ordinary skill in the art, knowledge of an associated regulatory region-regulatory protein pair can also be used to modulate expression of endogenous sequences of interest that are operably linked to endogenous regulatory regions. In such cases, a method of modulating expression of a sequence of interest includes transforming a plant cell that includes an endogenous regulatory region as described herein, with a recombinant nucleic acid construct comprising a nucleic acid encoding a regulatory protein as described herein, where the regulatory region and the regulatory protein are associated as indicated in Table 4 (in Example 2) and as described herein. A method for expressing an endogenous sequence of interest can include growing such a plant cell under conditions effective for expression of the regulatory protein. An endogenous sequence of interest can in certain cases be a nucleic acid encoding a polypeptide involved in lignin biosynthesis, such as a lignin biosynthesis enzyme or a regulatory protein involved in lignin biosynthesis.

In some cases, knowledge of an associated regulatory region-regulatory protein pair can be used to modulate expression of exogenous sequences of interest by endogenous regulatory proteins. Such a method can include transforming a plant cell that includes a nucleic acid encoding a regulatory protein as described herein, with a recombinant nucleic acid construct comprising a regulatory region described herein, where the regulatory region is operably linked to a sequence of interest, and where the regulatory region and the regulatory protein are associated as shown in Table 4 (in Example 2) and described herein. A method of expressing a sequence of interest can include growing such a plant cell under conditions effective for expression of the endogenous regulatory protein.

Also provided are methods for modulating the amount of lignin in a plant. Such a method can include growing a plant cell that includes a nucleic acid encoding an exogenous regulatory protein as described herein and an endogenous regulatory region as described herein operably linked to a sequence of interest. The regulatory protein and regulatory region are associated, as described previously. A sequence of interest can encode a polypeptide involved in lignin biosynthesis. A plant cell can be from a plant capable of producing lignin. The plant cell can be grown under conditions effective for expression of the regulatory protein. The lignin produced can be a novel lignin, e.g., not normally produced in a wild-type plant cell.

In some cases, a method for modulating the amount of lignin in a plant can include growing a plant cell that includes a nucleic acid encoding an endogenous regulatory protein as described herein and a nucleic acid including an exogenous regulatory region as described herein operably linked to a sequence of interest. A sequence of interest can encode a polypeptide involved in lignin biosynthesis. A plant cell can be grown under conditions effective for expression of the regulatory protein. The lignin produced can be a novel type of lignin, e.g., not normally produced in a wild-type plant cell. In some embodiments, a sequence of interest can be in an antisense orientation relative to the exogenous regulatory region. In some cases, a sequence of interest can be transcribed into an interfering RNA.

Provided herein also are methods for modulating (e.g., altering, increasing, or decreasing) the lignin content in a plant. The method can include growing a plant cell as described above, e.g., a plant cell that includes a nucleic acid encoding an endogenous or exogenous regulatory protein, where the regulatory protein associates with, respectively, an exogenous or endogenous regulatory region operably linked to a sequence of interest. In such cases, a sequence of interest can encode a polypeptide involved in lignin biosynthesis. Alternatively, a sequence of interest can result in a transcription product such as an antisense RNA or interfering RNA that affects lignin biosynthesis pathways, e.g., by modulating the steady-state level of mRNA transcripts available for translation that encode one or more lignin biosynthesis enzymes.

The materials and methods described herein are useful for modifying biomass characteristics, such as characteristics of biomass renewable energy source plants. A biomass renewable energy source plant is a plant having or producing material (either raw or processed) that comprises stored solar energy that can be converted to fuel. In general terms, such plants comprise dedicated energy crops as well as agricultural and woody plants. Examples of biomass renewable energy source plants include: switchgrass, elephant grass, giant chinese silver grass, energycane, giant reed (also known as wild cane), miscanthus, tall fescue, bermuda grass, sorghum, napier grass (also known as uganda grass), triticale, rye, winter wheat, shrub poplar, shrub willow, big bluestem, reed canary grass, and corn.

Articles of Manufacture

Transgenic plants provided herein have particular uses in agricultural industries. For example, transgenic plants, e.g., trees, described herein can be used to produce wood that is more lignified, and therefore more durable, than wood from corresponding wild-type plants. Such wood can serve as a superior wood fuel and/or raw material for applications such as woodworking. Transgenic plants such as trees having increased lignin content can also serve as sinks for carbon in the biosphere. Increased sequestration of carbon as lignin in transgenic plants may reduce atmospheric carbon dioxide and global warming. Transgenic plants can also be used to produce crops having an increased lignin content that are less susceptible to lodging. Increasing lignin in fruit, such as tomatoes, can increase the firmness of the fruit, thereby making it more amenable to shipping, storing, slicing, and dicing.

Also provided herein are transgenic plants, such as trees, having a reduced lignin content, which can be useful, e.g., to reduce the pulping cost and energy consumption in the pulping process used to make paper from wood. In addition, transgenic plants having a reduced lignin content can produce crops that are more digestible than crops produced from wild-type plants, which, in turn, can impact the livestock industry. Feeding dairy cattle corn silage produced from corn plants having a reduced and altered lignin content due to homozygosity at one or more bm loci can improve milk production (See, U.S. Pat. No. 6,114,609). Plants having a reduced lignin content also can be valuable for the production of biofuels. The crosslinking structure of lignin is known to complex with cellulose and hemicellulose, thus limiting the efficiency of the conversion process to produce ethanol from plant material. Reducing the lignin content in plants may increase the yield of ethanol from the plant material. See, for example, Mooney et al., Bioresour Technol, 64:113-119 (1998); Bernardez et al., Biotechnol Bioeng., 42:899-907 (1993); Chemoglazov et al., Enzyme Microbiol Technol, 10:503-507 (1988); and Vinzant et al., Appl Biochem Biotechnol, 62:99-104 (1997).

Lignin itself, which can be harvested from transgenic plants provided herein, can be converted into valuable fuel additives. Lignin can be removed from wood pulp of transgenic trees having an increased lignin content, and lignin can be recovered from any bioethanol production process using agricultural materials such as straw, corn stalks and switchgrass engineered to have an increased lignin content. Lignin can also be combusted to provide heat and/or power for the ethanol process; however, increasing the value of the lignin by converting it to higher value fuel additives can significantly enhance the competitiveness of bioethanol technology. Lignins removed from wood pulp as sulphates can be used as dust suppression agents for roads, as dispersants in high performance cement applications, water treatment formulations, and textile dyes, or as raw materials for several chemicals, such as vanillin, DMSA, ethanol, torula yeast, xylitol sugar, and humic acid.

Seeds of transgenic plants described herein can be conditioned and bagged in packaging material by means known in the art to form an article of manufacture. Packaging material such as paper and cloth are well known in the art. A package of seed can have a label e.g., a tag or label secured to the packaging material, a label printed on the packaging material, or a label inserted within the package. The package label may indicate that the seed herein incorporates transgenes that provide increased amounts of lignin in one or more tissues of plants grown from such seeds.

The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES Example 1 Generation of Lignin Regulatory Region::Luciferase Constructs and Regulatory Protein Constructs

Regulatory regions from genes encoding enzymes involved in phenylpropanoid (e.g., lignin) biosynthesis in Populus trichocarpa were examined for their ability to associate with regulatory proteins. Regulatory regions from each of the genes listed in Table 2 were amplified from Populus trichocarpa genomic DNA using PCR. Nucleotide sequences of the cloned regulatory regions are set forth in SEQ ID NOs:1909-1918.

TABLE 2 Regulatory regions isolated from Populus trichocarpa genes encoding enzymes involved in lignin biosynthesis Regulatory Region Regulatory SEQ Region Enzyme ID NO: Pt-4CL 4-Coumaroyl:CoA ligase 1909 Pt-F5H1 Ferulate 5-hydroxylase 1912 Pt-CCR1 Cinnamoyl-CoA reductase 1918 Pt-C4H Cinnamate 4-hydroxylase 1916 Pt-PAL4 Phenylalanine ammonia 1910 lyase Pt-CAD6 Cinnamyl alcohol 1915 dehydrogenase Pt-HCT Hydroxycinnamoyl 1911 transferase Pt-C3H1 p-Coumarate 3- 1917 hydroxylase Pt-COMT Caffeic acid O- 1913 methyltransferase Pt-CCoAOMT1 Caffeoyl-CoA O- 1914 methyltransferase

T-DNA binary vector constructs were made using standard molecular biology techniques. A set of constructs was generated using multi-site gateway cloning that contained a luciferase coding sequence operably linked to one of the regulatory regions set forth in Table 2 and SEQ ID NOs:1909-1918. Each of these constructs also contained a marker gene conferring resistance to the herbicide Finale®.

T-DNA binary vector constructs containing nucleic acids encoding regulatory proteins also were generated. Each construct contained a nucleic acid encoding one of the regulatory proteins listed in Table 4 (in Example 2) operably linked to a promoter. A CaMV 35S promoter was operably linked to each regulatory protein coding sequence with the following exception. Gemini ID 5217H1 (SEQ ID NO:1891) was operably linked to the 326F promoter. Each T-DNA binary vector construct was transformed into Agrobacterium. One colony from each transformation was selected and maintained as a glycerol stock. Five μL of the glycerol stock of each transformant were inoculated into 800 μL of YEB broth containing 80 μg/mL spectinomycin and 80 μg/mL rifampicin. The cultures were grown overnight in an incubator-shaker at 28° C. and harvested by centrifugation at 4,000 rpm for 15 minutes. The supernatants were discarded, and each pellet was resuspended in sterilized water to an optical density (OD₆₀₀) of about 0.05 to 0.1.

Example 2 Co-Infection Experiments in Nicotiana Plants

Wild-type Nicotiana tabaccum seeds were planted in 72-well trays containing a 60:40 (v:v) mixture of Sunshine mix and coarse vermiculite with six tablespoons of Marathon™ and nine tablespoons of Osmocote™ per 45 liters of Sunshine mix. The 72-well trays were covered with clear plastic propagation domes. Two weeks after planting, the domes were removed and plants in excess of one plant per well were removed. Four to five weeks after planting, the tobacco seedlings were co-infected with a mixture of two different Agrobacterium cultures described in Example 1. One of the Agrobacterium cultures contained a vector comprising a regulatory region listed in Table 2 operably linked to a luciferase reporter gene, and the other culture contained a vector that included a nucleotide sequence encoding a regulatory protein listed in Table 4 operably linked to a promoter. Two hundred μL of each of the two different Agrobacterium suspensions were mixed together. The mixture was loaded into a 1 mL syringe without a needle and infused in duplicate on the underside of a Nicotiana leaf. Each Agrobacterium suspension containing a regulatory region listed in Table 2 operably linked to a luciferase reporter gene, or a nucleotide sequence encoding a regulatory protein listed in Table 4 operably linked to a promoter, was infused separately on the underside of the same Nicotiana leaf as a control for background luciferase expression and as a negative control, respectively. Two leaves per tobacco seedling were infused. The plants were incubated in a greenhouse for two to four days.

Leaves of Nicotiana plants that were infused with Agrobacterium were removed from the plants, the non-infused regions of the leaves were trimmed, and the trimmed leaves were arranged in 150×15 mm Petri dishes containing 1% agarose gel. The leaves were sprayed with 1 mM beetle luciferin (catalog no. E1602, Promega, Madison, Wis.) in 0.01% Triton X-100. The Petri dishes were then placed on the stage inside the chamber a Night Owl™ CCD camera (Berthold Technology, Oak Ridge, Tenn.) for about one or two minutes to minimize autofluorescence. Luciferase images were acquired using a one minute exposure time, and a two minute and a five minute exposure time if the signal was low. After acquiring the luciferase images, bright field images also were acquired using a 20 millisecond exposure time.

Qualitative scoring of luciferase reporter activity from each infused leaf was done by visual inspection and comparison of images, taking into account whether or not the luminescence signal in the portions of the leaf that were infused with a mixture of Agrobacterium cultures, containing both the regulatory region and the regulatory protein constructs, was higher than the luminescence signal in the portion of the leaf infused with either culture independently. Results of the visual inspection were noted according to the rating system listed in Table 3, and with respect to both the positive and negative controls.

TABLE 3 Luciferase activity scoring system Score Score Comment +++ signal in the co-infected portion of the leaf is much stronger than in the background control portion of the leaf ++ signal in the co-infected portion of the leaf is stronger than in the background control portion of the leaf + signal in the co-infected portion of the leaf is somewhat stronger than in the background control portion of the leaf +/− signal in the co-infected portion of the leaf is weak, but still stronger than in the background control portion of the leaf − no detectable signal

Lignin regulatory region/regulatory protein combinations, also referred to as associations herein, that resulted in a score of ++ or +++ in Nicotiana co-infection experiments are listed in Table 4.

TABLE 4 Combinations of regulatory regions and regulatory proteins producing expression of a reporter gene operably linked to each regulatory region Regulatory Regulatory Regulatory Regulatory Regulatory Regulatory Protein Regulatory Protein Protein Protein Protein Protein Source Region SEQ ID NO: Gemini_ID Clone_ID Annot_ID Locus ID Organism Pt4CL 1862 532E10 2767 At3g25930 Arabidopsis thaliana Pt4CL 1828 5110C1 841947 At3g24070 Arabidopsis thaliana Pt4CL 1822 5110D6 541941 At1g03840 Arabidopsis thaliana Pt4CL 157 5110G4 568299 At5g01980 Arabidopsis thaliana Pt4CL 159 5110H1 574716 At5g55690 Arabidopsis thaliana Pt4CL 165 5110H6 840236 At3g10490 Arabidopsis thaliana Pt4CL 1767 531A5 32791 At4g09960 Arabidopsis thaliana Pt4CL 1064 531B4* 6042 At4g17500 Arabidopsis thaliana Pt4CL 1860 531F2* 266712 At4g39260 Arabidopsis thaliana Pt4CL 1595 531F6 41439 At3g19580 Arabidopsis thaliana Pt4CL 1882 531G11 605218 Glycine max Pt4CL 1886 531H11* 625035 Glycine max Pt4CL 1573 531H5 36272 At1g54830 Arabidopsis thaliana Pt4CL 1444 531H7 16204 At4g35570 Arabidopsis thaliana Pt4CL 1897 531H8 5398 At1g15100 Arabidopsis thaliana Pt4CL 1475 531H9 21374 At4g22745 Arabidopsis thaliana Pt4CL 1836 533D3 114074 At5g42630 Arabidopsis thaliana Pt4CL 1249 533F7 21604 At3g48590 Arabidopsis thaliana Pt4CL 671 533H10 2942 At3g07565 Arabidopsis thaliana Pt4CL 1581 539A11 389585 Zea mays subsp. mays Pt4CL 1383 539B6 115924 At2g01060 Arabidopsis thaliana Pt4CL 518 539F5 157740 At3g25790 Arabidopsis thaliana Pt4CL 1052 540H7 557009 Glycine max Pt4CL 583 555C3 222885 Zea mays subsp. mays PtC3H 170 5110E5* 844490 At3g55340 Arabidopsis thaliana PtC3H 134 5109A8 550729 At2g04240 Arabidopsis thaliana PtC3H 1728 5109C6 574705 At5g55580 Arabidopsis thaliana PtC3H 104 5109H7 542746 At1g10585 Arabidopsis thaliana PtC3H 1828 5110C1 841947 At3g24070 Arabidopsis thaliana PtC3H 157 5110G4 568299 At5g01980 Arabidopsis thaliana PtC3H 165 5110H6 840236 At3g10490 Arabidopsis thaliana PtC3H 520 531B2 158240 At3g14230 Arabidopsis thaliana PtC3H 1832 531F1 106887 At1g62990 Arabidopsis thaliana PtC3H 1882 531G11* 605218 Glycine max PtC3H 548 532A12 1845 At2g14900 Arabidopsis thaliana PtC3H 590 532C7 22671 Arabidopsis thaliana PtC3H 1692 532F1 92102 At5g61600 Arabidopsis thaliana PtC3H 808 532H8 37980 At2g47450 Arabidopsis thaliana PtC3H 885 534A3 41634 At3g54810 Arabidopsis thaliana PtC3H 614 534C10 2831 At3g62420 Arabidopsis thaliana PtC3H 221 534F12 1011900 At2g21660 Arabidopsis thaliana PtC3H 1526 535B8 26867 At1g22810 Arabidopsis thaliana PtC3H 417 535G9 12256 At4g16265 Arabidopsis thaliana PtC3H 1854 535H2 25793 At4g31720 Arabidopsis thaliana PtC3H 678 536C10 299144 Zea mays subsp. mays PtC3H 1211 539F4 14909 At3g62290 Arabidopsis thaliana PtC3H 1830 539F6 100085 At5g14000 Arabidopsis thaliana PtC3H 1239 552A11 19340 At3g60800 Arabidopsis thaliana PtC3H 1323 552C9 225321 Zea mays subsp. mays PtC3H 610 553H11 25816 At3g04070 Arabidopsis thaliana PtC3H 1653 553H5 660003 Glycine max PtC4H 1414 555E5 12997 At5g45100 Arabidopsis thaliana PtC4H 1610 531E8 42530 At1g72730 Arabidopsis thaliana PtC4H 1377 531E9 108109 At1g68520 Arabidopsis thaliana PtC4H 833 539E10 388074 Zea mays subsp. mays PtC4H 1806 531A7 519 At1g74500 Arabidopsis thaliana PtC4H 1752 531F11 603410 Glycine max PtC4H 1661 531F12 681088 Glycine max PtC4H 885 534A3 41634 At3g54810 Arabidopsis thaliana PtC4H 1469 534G9 20769 At4g24470 Arabidopsis thaliana PtC4H 1906 534H5 9325 At1g06680 Arabidopsis thaliana PtC4H 2065 536F6 9804 At2g02080 Arabidopsis thaliana PtC4H 585 536H10 224919 Zea mays subsp. mays PtC4H 1315 538B5 208429 Zea mays subsp. mays PtC4H 1585 539D12 397320 Zea mays subsp. mays PtC4H 2085 539D9 362993 Zea mays subsp. mays PtC4H 1058 540B5 558003 Glycine max PtC4H 914 540B6 479006 Glycine max PtC4H 1878 540C4 558431 Glycine max PtC4H 566 553A11 21406 At1g05805 Arabidopsis thaliana PtC4H 760 553A7 34635 At3g54340 Arabidopsis thaliana PtC4H 1552 553C11 33333 At4g21440 Arabidopsis thaliana PtC4H 1904 553D4 33016 At1g22070 Arabidopsis thaliana PtC4H 703 553F1 33139 At3g28910 Arabidopsis thaliana PtC4H 964 553H3 539801 Glycine max PtC4H 1653 553H5 660003 Glycine max PtC4H 1481 553H9 21863 At5g59550 Arabidopsis thaliana PtC4H 1518 554G8 25795 At2g46410 Arabidopsis thaliana PtC4H 583 555C3 222885 Zea mays subsp. mays PtC4H 835 555F10 38961 At5g18090 Arabidopsis thaliana PtC4H 379 555F8 115358 At2g40340 Arabidopsis thaliana PtC4H 339 555H5 105162 At1g55910 Arabidopsis thaliana PtCAD6 1165 532E2 99033 At5g58787 Arabidopsis thaliana PtCAD6 370 539E6 112194 At1g78600 Arabidopsis thaliana PtCAD6 1874 540E6 474636 Glycine max PtCAD6 555 536E7 205648 At1g56010 Arabidopsis thaliana PtCAD6 833 539E10 388074 Zea mays subsp. mays PtCAD6 415 553E10 119790 At4g35550 Arabidopsis thaliana PtCAD6 374 553E12 113639 At3g47500 Arabidopsis thaliana PtCAD6 149 5109G6 554970 At2g41460 Arabidopsis thaliana PtCAD6 1722 5109H3 552542 At2g21320 Arabidopsis thaliana PtCAD6 1735 5110H5 834509 At1g32150 Arabidopsis thaliana PtCAD6 1785 531A9 8607 At5g15160 Arabidopsis thaliana PtCAD6 520 531B2 158240 At3g14230 Arabidopsis thaliana PtCAD6 606 531C8 2499 At5g25890 Arabidopsis thaliana PtCAD6 1842 532A5 152630 At1g16490 Arabidopsis thaliana PtCAD6 461 532B12 1480 At5g20240 Arabidopsis thaliana PtCAD6 590 532C7 22671 Arabidopsis thaliana PtCAD6 1504 532H5 251466 At5g52020 Arabidopsis thaliana PtCAD6 838 532H9 3900 At1g05710 Arabidopsis thaliana PtCAD6 1163 533A2 98716 At1g25330 Arabidopsis thaliana PtCAD6 172 533A9 1001761 At5g09250 Arabidopsis thaliana PtCAD6 1850 534D12 231890 Arabidopsis thaliana PtCAD6 413 534F6 119460 At3g04060 Arabidopsis thaliana PtCAD6 1469 534G9 20769 At4g24470 Arabidopsis thaliana PtCAD6 1570 535F5 34589 At1g74430 Arabidopsis thaliana PtCAD6 337 536B6 104839 At2g14490 Arabidopsis thaliana PtCAD6 638 536G9 285598 Zea mays subsp. mays PtCAD6 585 536H10 224919 Zea mays subsp. mays PtCAD6 1333 538C6 333753 Zea mays subsp. mays PtCAD6 686 538H5 312833 Zea mays subsp. mays PtCAD6 1564 538H6 333416 Zea mays subsp. mays PtCAD6 1585 539D12 397320 Zea mays subsp. mays PtCAD6 779 539G8 362438 Zea mays subsp. mays PtCAD6 2087 539H3 28026 At1g07980 Arabidopsis thaliana PtCAD6 1779 540A8 541719 Glycine max PtCAD6 1878 540C4 558431 Glycine max PtCAD6 1876 552A4 520515 Glycine max PtCAD6 601 552A6 240112 Zea mays subsp. mays PtCAD6 1062 552A8 560961 Glycine max PtCAD6 1864 552C6* 280261 Zea mays subsp. mays PtCAD6 1868 552H9 284030 Zea mays subsp. mays PtCAD6 566 553A11 21406 At1g05805 Arabidopsis thaliana PtCAD6 1884 553B10 6163 At3g62690 Arabidopsis thaliana PtCAD6 1259 553C3 29637 At1g13690 Arabidopsis thaliana PtCAD6 1653 553H5* 660003 Glycine max PtCAD6 1129 554D11 93825 At3g61950 Arabidopsis thaliana PtCAD6 680 554G6 31044 At2g44940 Arabidopsis thaliana PtCCoAOMT 1165 532E2 99033 At5g58787 Arabidopsis thaliana PtCCoAOMT 1610 531E8 42530 At1g72730 Arabidopsis thaliana PtCCoAOMT 372 555E8 113443 At2g05440 Arabidopsis thaliana PtCCoAOMT 1785 531A9 8607 At5g15160 Arabidopsis thaliana PtCCoAOMT 606 531C8 2499 At5g25890 Arabidopsis thaliana PtCCoAOMT 1595 531F6 41439 At3g19580 Arabidopsis thaliana PtCCoAOMT 1183 532G2 99612 At4g32800 Arabidopsis thaliana PtCCoAOMT 1104 533F11 8334 At3g29035 Arabidopsis thaliana PtCCoAOMT 432 533H4 123804 At4g09040 Arabidopsis thaliana PtCCoAOMT 1872 535A8 35890 At5g46690 Arabidopsis thaliana PtCCoAOMT 1405 535A9 12071 At1g53160 Arabidopsis thaliana PtCCoAOMT 652 535H5 2898 At1g43890 Arabidopsis thaliana PtCCoAOMT 599 539H2 231109 At5g29000 Arabidopsis thaliana PtCCoAOMT 2087 539H3 28026 At1g07980 Arabidopsis thaliana PtCCoAOMT 1540 552D1* 325800 Zea mays subsp. mays PtCCoAOMT 355 554A9 110419 At4g33565 Arabidopsis thaliana PtCCoAOMT 1267 554B7 34414 At2g47170 Arabidopsis thaliana PtCCoAOMT 504 554D10 156373 At3g11200 Arabidopsis thaliana PtCCoAOMT 407 554D2 117643 At1g74840 Arabidopsis thaliana PtCCoAOMT 816 554D4 38360 At4g22750 Arabidopsis thaliana PtCCoAOMT 835 555F10 38961 At5g18090 Arabidopsis thaliana PtCCoAOMT 1870 555G3 306139 Zea mays subsp. mays PtCCoAOMT 1848 555G5* 21674 At3g55330 Arabidopsis thaliana PtCCR1 1722 5109H3 552542 At2g21320 Arabidopsis thaliana PtCCR1 96 5110G12 541887 At1g03360 Arabidopsis thaliana PtCCR1 1637 531A4 6397 At2g44840 Arabidopsis thaliana PtCCR1 1806 531A7 519 At1g74500 Arabidopsis thaliana PtCCR1 524 531A8* 15990 At3g44750 Arabidopsis thaliana PtCCR1 1661 531F12* 681088 Glycine max PtCCR1 1573 531H5 36272 At1g54830 Arabidopsis thaliana PtCCR1 1444 531H7 16204 At4g35570 Arabidopsis thaliana PtCCR1 1096 532C9 7774 At3g03270 Arabidopsis thaliana PtCCR1 1423 532D11* 14246 At3g52380 Arabidopsis thaliana PtCCR1 1183 532G2 99612 At4g32800 Arabidopsis thaliana PtCCR1 808 532H8 37980 At2g47450 Arabidopsis thaliana PtCCR1 838 532H9 3900 At1g05710 Arabidopsis thaliana PtCCR1 1836 533D3 114074 At5g42630 Arabidopsis thaliana PtCCR1 1844 534G10 19561 At1g68840 Arabidopsis thaliana PtCCR1 1469 534G9 20769 At4g24470 Arabidopsis thaliana PtCCR1 1570 535F5 34589 At1g74430 Arabidopsis thaliana PtCCR1 652 535H5 2898 At1g43890 Arabidopsis thaliana PtCCR1 678 536C10 299144 Zea mays subsp. mays PtCCR1 1628 537H2 560731 Glycine max PtCCR1 707 538F5 331755 Zea mays subsp. mays PtCCR1 744 538G9* 339518 Zea mays subsp. mays PtCCR1 695 538H10 325679 Zea mays subsp. mays PtCCR1 686 538H5 312833 Zea mays subsp. mays PtCCR1 934 540B2 479015 Glycine max PtCCR1 938 540F4 534281 Glycine max PtCCR1 1345 540H1 475689 Glycine max PtCCR1 994 540H5 543118 Glycine max PtCCR1 1052 540H7 557009 Glycine max PtCCR1 601 552A6 240112 Zea mays subsp. mays PtCCR1 1540 552D1 325800 Zea mays subsp. mays PtCCR1 381 552H11 115366 At3g14100 Arabidopsis thaliana PtCCR1 760 553A7 34635 At3g54340 Arabidopsis thaliana PtCCR1 1884 553B10 6163 At3g62690 Arabidopsis thaliana PtCCR1 1698 553C6* 968026 Brassica napus PtCCR1 355 554A9 110419 At4g33565 Arabidopsis thaliana PtCCR1 1518 554G8 25795 At2g46410 Arabidopsis thaliana PtCCR1 1395 555C1 120302 At4g38620 Arabidopsis thaliana PtCCR1 1675 553H6 691319 Glycine max PtCCR1 1473 553C1 21240 At5g25220 Arabidopsis thaliana PtCOMT 898 536E6 41875 At2g01760 Arabidopsis thaliana PtCOMT 163 5109E9 830468 At2g44330 Arabidopsis thaliana PtCOMT 833 539E10 388074 Zea mays subsp. mays PtCOMT 1722 5109H3 552542 At2g21320 Arabidopsis thaliana PtCOMT 1826 5109H5 566835 At4g28990 Arabidopsis thaliana PtCOMT 1892 5217H1 Populus trichocarpa PtCOMT 1371 531B11 597624 Glycine max PtCOMT 730 531C5 33435 At4g29020 Arabidopsis thaliana PtCOMT 606 531C8 2499 At5g25890 Arabidopsis thaliana PtCOMT 689 531C9 31322 At4g35570 Arabidopsis thaliana PtCOMT 1681 531D4* 7559 At1g09140 Arabidopsis thaliana PtCOMT 781 535B5 36370 At3g14110 Arabidopsis thaliana PtCOMT 1526 535B8 26867 At1g22810 Arabidopsis thaliana PtCOMT 417 535G9 12256 At4g16265 Arabidopsis thaliana PtCOMT 608 535H10 25211 At5g44080 Arabidopsis thaliana PtCOMT 1361 537A3 560948 Glycine max PtCOMT 2085 539D9 362993 Zea mays subsp. mays PtCOMT 1052 540H7 557009 Glycine max PtCOMT 1239 552A11 19340 At3g60800 Arabidopsis thaliana PtCOMT 1323 552C9 225321 Zea mays subsp. mays PtCOMT 1518 554G8 25795 At2g46410 Arabidopsis thaliana PtCOMT 1435 555B2 149496 At1g04990 Arabidopsis thaliana PtF5H1 119 5109B4 549656 At1g75510 Arabidopsis thaliana PtF5H1 1806 531A7 519 At1g74500 Arabidopsis thaliana PtF5H1 1785 531A9 8607 At5g15160 Arabidopsis thaliana PtF5H1 1371 531B11 597624 Glycine max PtF5H1 1185 531B7* 3929 At2g05440 Arabidopsis thaliana PtF5H1 730 531C5 33435 At4g29020 Arabidopsis thaliana PtF5H1 1661 531F12 681088 Glycine max PtF5H1 1860 531F2 266712 At4g39260 Arabidopsis thaliana PtF5H1 1692 532F1 92102 At5g61600 Arabidopsis thaliana PtF5H1 445 532G6 14203 At2g27580 Arabidopsis thaliana PtF5H1 526 533G9 16284 At1g51070 Arabidopsis thaliana PtF5H1 361 533H2 112098 At1g67950 Arabidopsis thaliana PtF5H1 1850 534D12 231890 Arabidopsis thaliana PtF5H1 1526 535B8 26867 At1g22810 Arabidopsis thaliana PtF5H1 1570 535F5 34589 At1g74430 Arabidopsis thaliana PtF5H1 1315 538B5 208429 Zea mays subsp. mays PtF5H1 707 538F5 331755 Zea mays subsp. mays PtF5H1 1866 538H1 280814 Zea mays subsp. mays PtF5H1 357 539A7 110428 At3g19500 Arabidopsis thaliana PtF5H1 1876 552A4 520515 Glycine max PtF5H1 566 553A11 21406 At1g05805 Arabidopsis thaliana PtF5H1 1302 554A1 124720 At3g20310 Arabidopsis thaliana PtF5H1 355 554A9 110419 At4g33565 Arabidopsis thaliana PtF5H1 793 554C4 37739 At2g27820 Arabidopsis thaliana PtF5H1 698 554G1 32754 At4g35785 Arabidopsis thaliana PtF5H1 1620 554G4* 45 At4g12040 Arabidopsis thaliana PtF5H1 1518 554G8 25795 At2g46410 Arabidopsis thaliana PtF5H1 1840 554H2* 14432 At3g49760 Arabidopsis thaliana PtF5H1 1081 555B4* 626054 Glycine max PtF5H1 1395 555C1 120302 At4g38620 Arabidopsis thaliana PtF5H1 490 555C11 156298 At1g24440 Arabidopsis thaliana PtF5H1 1285 531C6 38311 At1g25560 Arabidopsis thaliana PtF5H1 1421 535G10 13930 At5g02590 Arabidopsis thaliana PtHCT 415 553E10 119790 At4g35550 Arabidopsis thaliana PtHCT 106 5110B11 548715 At1g67340 Arabidopsis thaliana PtHCT 1824 5110C9 543489 At1g16880 Arabidopsis thaliana PtHCT 1493 532G5 250132 At1g12440 Arabidopsis thaliana PtHCT 409 532H3 118001 At1g12860 Arabidopsis thaliana PtHCT 1504 532H5 251466 At5g52020 Arabidopsis thaliana PtHCT 808 532H8 37980 At2g47450 Arabidopsis thaliana PtHCT 1083 533B10 6639 At5g57660 Arabidopsis thaliana PtHCT 661 533B11 2913 At1g69780 Arabidopsis thaliana PtHCT 1249 533F7 21604 At3g48590 Arabidopsis thaliana PtHCT 652 535H5 2898 At1g43890 Arabidopsis thaliana PtHCT 337 536B6 104839 At2g14490 Arabidopsis thaliana PtHCT 638 536G9 285598 Zea mays subsp. mays PtHCT 1060 537H3 560765 Glycine max PtHCT 1858 539C3 261272 At1g17970 Arabidopsis thaliana PtHCT 1852 539C4 250028 At1g24210 Arabidopsis thaliana PtHCT 1888 539D2 6827 At5g47520 Arabidopsis thaliana PtHCT 518 539F5* 157740 At3g25790 Arabidopsis thaliana PtHCT 1830 539F6 100085 At5g14000 Arabidopsis thaliana PtHCT 438 539F7* 125917 At4g39470 Arabidopsis thaliana PtHCT 436 539H7 124496 At1g30210 Arabidopsis thaliana PtHCT 936 540A4 531573 Glycine max PtHCT 1131 552B2* 963031 Brassica napus PtHCT 1890 552C2 969682 Brassica napus PtHCT 1323 552C9 225321 Zea mays subsp. mays PtHCT 1050 552G4 545182 Glycine max PtHCT 1868 552H9* 284030 Zea mays subsp. mays PtHCT 703 553F1 33139 At3g28910 Arabidopsis thaliana PtPAL4 1414 555E5 12997 At5g45100 Arabidopsis thaliana PtPAL4 370 539E6 112194 At1g78600 Arabidopsis thaliana PtPAL4 1874 540E6 474636 Glycine max PtPAL4 737 538E7 337432 Zea mays subsp. mays PtPAL4 372 555E8 113443 At2g05440 Arabidopsis thaliana PtPAL4 1377 531E9 108109 At1g68520 Arabidopsis thaliana PtPAL4 1862 532E10 2767 At3g25930 Arabidopsis thaliana PtPAL4 833 539E10 388074 Zea mays subsp. mays PtPAL4 374 553E12 113639 At3g47500 Arabidopsis thaliana PtPAL4 119 5109B4 549656 At1g75510 Arabidopsis thaliana PtPAL4 161 5109B8 829219 At2g34200 Arabidopsis thaliana PtPAL4 1637 531A4 6397 At2g44840 Arabidopsis thaliana PtPAL4 1767 531A5 32791 At4g09960 Arabidopsis thaliana PtPAL4 1806 531A7 519 At1g74500 Arabidopsis thaliana PtPAL4 1785 531A9 8607 At5g15160 Arabidopsis thaliana PtPAL4 1185 531B7 3929 At2g05440 Arabidopsis thaliana PtPAL4 689 531C9 31322 At4g35570 Arabidopsis thaliana PtPAL4 1681 531D4 7559 At1g09140 Arabidopsis thaliana PtPAL4 1475 531H9 21374 At4g22745 Arabidopsis thaliana PtPAL4 548 532A12 1845 At2g14900 Arabidopsis thaliana PtPAL4 1842 532A5 152630 At1g16490 Arabidopsis thaliana PtPAL4 461 532B12 1480 At5g20240 Arabidopsis thaliana PtPAL4 411 532C4 118756 At1g14260 Arabidopsis thaliana PtPAL4 590 532C7 22671 Arabidopsis thaliana PtPAL4 1096 532C9 7774 At3g03270 Arabidopsis thaliana PtPAL4 865 532D10 40334 At5g20240 Arabidopsis thaliana PtPAL4 1423 532D11 14246 At3g52380 Arabidopsis thaliana PtPAL4 1692 532F1 92102 At5g61600 Arabidopsis thaliana PtPAL4 1183 532G2 99612 At4g32800 Arabidopsis thaliana PtPAL4 1493 532G5 250132 At1g12440 Arabidopsis thaliana PtPAL4 445 532G6 14203 At2g27580 Arabidopsis thaliana PtPAL4 465 532H11 1492 At5g47200 Arabidopsis thaliana PtPAL4 409 532H3 118001 At1g12860 Arabidopsis thaliana PtPAL4 838 532H9 3900 At1g05710 Arabidopsis thaliana PtPAL4 1163 533A2 98716 At1g25330 Arabidopsis thaliana PtPAL4 1838 533B6 143475 At4g36570 Arabidopsis thaliana PtPAL4 405 533C4 116968 At2g37580 Arabidopsis thaliana PtPAL4 1836 533D3 114074 At5g42630 Arabidopsis thaliana PtPAL4 1104 533F11 8334 At3g29035 Arabidopsis thaliana PtPAL4 1249 533F7 21604 At3g48590 Arabidopsis thaliana PtPAL4 526 533G9 16284 At1g51070 Arabidopsis thaliana PtPAL4 671 533H10 2942 At3g07565 Arabidopsis thaliana PtPAL4 361 533H2 112098 At1g67950 Arabidopsis thaliana PtPAL4 1872 535A8 35890 At5g46690 Arabidopsis thaliana PtPAL4 852 535C4 39855 At2g36930 Arabidopsis thaliana PtPAL4 1361 537A3 560948 Glycine max PtPAL4 1628 537H2 560731 Glycine max PtPAL4 1333 538C6 333753 Zea mays subsp. mays PtPAL4 1866 538H1 280814 Zea mays subsp. mays PtPAL4 695 538H10 325679 Zea mays subsp. mays PtPAL4 1564 538H6 333416 Zea mays subsp. mays PtPAL4 357 539A7 110428 At3g19500 Arabidopsis thaliana PtPAL4 1852 539C4 250028 At1g24210 Arabidopsis thaliana PtPAL4 1585 539D12 397320 Zea mays subsp. mays PtPAL4 1465 539D5 207419 At1g66810 Arabidopsis thaliana PtPAL4 599 539H2 231109 At5g29000 Arabidopsis thaliana PtPAL4 436 539H7 124496 At1g30210 Arabidopsis thaliana PtPAL4 914 540B6 479006 Glycine max PtPAL4 980 540F9 542773 Glycine max PtPAL4 900 540G8 478453 Glycine max PtPAL4 1052 540H7 557009 Glycine max PtPAL4 1131 552B2 963031 Brassica napus PtPAL4 1294 552G11 109490 At1g21450 Arabidopsis thaliana PtPAL4 381 552H11 115366 At3g14100 Arabidopsis thaliana PtPAL4 1880 552H7* 560898 Glycine max PtPAL4 1552 553C11 33333 At4g21440 Arabidopsis thaliana PtPAL4 1904 553D4 33016 At1g22070 Arabidopsis thaliana PtPAL4 703 553F1 33139 At3g28910 Arabidopsis thaliana PtPAL4 1302 554A1 124720 At3g20310 Arabidopsis thaliana PtPAL4 529 554B3* 17402 At2g23780 Arabidopsis thaliana PtPAL4 1267 554B7 34414 At2g47170 Arabidopsis thaliana PtPAL4 793 554C4 37739 At2g27820 Arabidopsis thaliana PtPAL4 504 554D10 156373 At3g11200 Arabidopsis thaliana PtPAL4 1129 554D11 93825 At3g61950 Arabidopsis thaliana PtPAL4 407 554D2 117643 At1g74840 Arabidopsis thaliana PtPAL4 816 554D4 38360 At4g22750 Arabidopsis thaliana PtPAL4 1620 554G4 45 At4g12040 Arabidopsis thaliana PtPAL4 680 554G6 31044 At2g44940 Arabidopsis thaliana *Indicates that the regulatory protein also was observed to be associated with the indicated regulatory region in a secondary screen in Populus, described below. Pt4CL = Populus 4-Coumaroyl:CoA ligase PtF5H1 = Populus Ferulate 5-hydroxylase PtCCR1 = Populus Cinnamoyl-CoA reductase PtC4H = Populus Cinnamate 4-hydroxylase PtPAL4 = Populus Phenylalanine ammonia lyase PtCAD6 = Populus Cinnamyl alcohol dehydrogenase PtHCT = Populus Hydroxycinnamoyl transferase PtC3H = Populus p-Coumarate 3-hydroxylase PtCOMT = Populus Caffeic acid O-methyltransferase PtCCoAOMT = Populus Caffeoyl-CoA O-methyltransferase

Certain regulatory proteins and regulatory regions have been tested in a secondary screen in Populus. The procedure used to perform the secondary screen in Populus was similar to that used to perform the primary screen in Nicotiana as described above, with the following modifications. About 17 μL of the glycerol stock of each Agrobacterium culture containing a vector comprising a regulatory region or a regulatory protein were inoculated into four mL of YEB medium containing spectinomycin and rifampicin. After growing overnight, each culture was harvested and resuspended to the original volume in an aqueous solution containing 10 mM MgCl₂, 10 mM MES (pH 5.7), and 150 μM acetosyringone.

Populus plants were grown in soil comprising a 60:40 mixture of Sunshine mix to coarse vermiculite, containing six tablespoons of Marathon™ and nine tablespoons of Osmocote™ per 45 liters of Sunshine mix. The plants were maintained in a greenhouse, zone C, and watered every other day. Once a week, the plants were watered with an aqueous solution containing Peter supplement. About 20 discs per leaf were punched from leaves of the Populus plants using a hole punch. The discs were placed in a Petri dish containing a mixture of two different Agrobacterium cultures, one containing a vector comprising a regulatory region listed in Table 2 operably linked to a luciferase reporter gene, and the other containing a vector including a nucleotide sequence encoding a regulatory protein listed in Table 4 operably linked to a promoter. Equal amounts (500 μL) of each Agrobacterium culture were mixed in the Petri dish with 12.5 mL of an aqueous solution containing 10 mM MgCl₂, 10 mM MES (pH 5.7), and 150 μM acetosyringone. For negative and background controls, leaf discs were placed in Petri dishes containing a single Agrobacterium culture with a vector including a nucleotide sequence encoding a regulatory protein or a vector including a regulatory region operably linked to a luciferase gene, respectively. Vacuum infiltration was performed for seven minutes at about 75% full-strength. A background control corresponding to the regulatory region being tested was included in the same vacuum infiltration setting. Upon completion of vacuum infiltration, the leaf discs were blot-dried on paper towels and transferred to square Petri dishes lined with paper towels wetted with MS medium (1×MS salt in ddH₂O, pH 5.7). The leaf discs were incubated for two to four days in a growth chamber (27° C., 16 hour light cycle) prior to CCD analysis as described above. Results of these experiments are presented in Table 4 above.

Based on the results presented above, expression of a sequence of interest can be modulated in a plant by operably linking a regulatory region from Table 2 to that sequence and controlling expression via one or more of the regulatory proteins that are associated with that regulatory region.

It will be appreciated that regulatory proteins other than those described herein can be screened to determine whether they associate with the regulatory regions of Table 2. That is, one of ordinary skill can use the techniques described herein to identify new regulatory region-regulatory protein association pairs.

Example 3 Histological Analysis of Lignin Content in Transgenic Arabidopsis Lines

Transgenic Arabidopsis lines transformed with nucleic acid constructs encoding regulatory proteins were analyzed for lignin content using histological staining. Each transgenic line that was analyzed is listed in Table 5 along with identifiers for the corresponding regulatory protein, the nucleic acid encoding the regulatory protein, and the promoter used to express the regulatory protein.

TABLE 5 Transgenic Arabidopsis lines analyzed for lignin content Regu- latory Transgenic Regulatory Regulatory Vector Protein Line Pro- Protein Protein Construct SEQ ID moter Clone ID Gemini ID ID ID NO: ME22388 PT0843 16204 572C1 35199513 1444 ME04442 35S 97001 216G3 1134 ME04932 35S 1003205 280D7 178 ME02500 35S 152630 162G10 14300834 1842 ME04445 35S 124720 216B4 14300682 1302 ME04024 35S 92102 159A3 14299950 1692 ME02589 35S 207629 83D4 1846 ME05057 35S 691319 284E8 1675 ME01535 35S 36272 87F4 14299254 1573 ME03502 35S 14246 179A12 14297678 1423 ME02276 35S 5398 113C2 14297012 1897 ME02013 35S 6042 107E8 14297067 1064 ME10647 35S 331755 527D4 21992337 707 ME08450 35S 240112 474E10 22795850 601 ME03301 35S 3900 178A7 14296905 838 ME01567 35S 38311 87B9 1285 ME00122 32449 117643 15D9 25357704 407 ME01486 35S 32791 86A9 14298935 1767 ME06485 35S 13930 332E3 1421 ME06492 35S 21240 332F4 1473 ME23571 326F 5217H1 1892 ME02171 35S 113443 110E9 14300413 372 ME12975 35S 118184 549H3 1393

Seeds from the transgenic lines listed in Table 5 were sown in a 60:40 mixture of Sunshine Mix #5 and coarse vermiculite. The sown seeds were stratified for at least three days in a refrigerated cabinet prior to germination in the greenhouse.

To test the staining protocol and determine the optimum developmental stage for histology screening, wild-type plants were collected at different time points starting from the seedling stage just after bolting, about 16 to 18 days after germination, up to the mature stage, about 35 days after germination. Based on the results of this analysis, which are summarized in Table 6 below, Arabidopsis plants were allowed to grow for at least 24 to 26 days post-germination prior to performing the primary histological analysis.

Some of the transgenic lines were analyzed further for ectopic lignin accumulation. Transgenic Arabidopsis seedlings were collected two weeks post germination and incubated overnight in a 12-well dish containing 80% ethanol to remove the chlorophyll. In addition, mature rosette and cauline leaves were collected from transgenic plants five weeks after germination, placed in a 12-well dish, and processed in a manner similar to the manner in which the seedlings were processed.

Phloroglucinol Staining

For the primary histological analysis, the main inflorescence stem was cut at the basal end, about 0.5 cm from the junction of the rosette leaves, using a razor blade. Thin sections of the stems, about 200 microns thick, were manually generated using a razor blade against a Styrofoam support. Up to three individual plants were sampled from each transformation event. Up to five transformation events per transgenic line were used.

The tissue sections were immediately placed on a microscope slide and a drop of 1% phloroglucinol solution in 6 M HCl was placed on top of each section to adequately cover the sample for about 2 minutes. The phloroglucinol reagent present in the tissue sections was diluted by adding about 5 drops of water using a pipette. A cover slip was placed on the tissue sections in preparation for microscopy, and any excess liquid was removed with a tissue paper.

For seedlings and whole leaf tissues, ethanol was removed after overnight incubation and replaced with 1 mL of 1% phloroglucinol solution in 6 M HCl to cover the tissues in the well. The tissues were stained for about 2 minutes. The phloroglucinol solution was subsequently removed and replaced with 1 mL of water. The tissues were kept in the 12-well dish for scanning.

Microscopy, Image Acquisition, and Image Analysis

Digital images of tissue sections were taken in tif format at 50× magnification using a Carl Zeiss Axioshop 2 microscope set in a dark field view at 3200K exposure. The microscope was linked to Axiovision software version 3.1.2.1 set at 3200K white balance exposure. The tif format images were adjusted and converted into jpeg format using the Adobe Photoshop plug-in software (AGD Color Temperature Correction version 4) set at 6000K correction condition.

The adjusted jpeg format images were read by WinRhizo Pro software (Regent Instruments Inc.) using a calibration method to classify the pixels within the image view according to whether they belonged to stained lignified cells/tissues (designated as X), to non-lignified cells/tissues (designated as NL), or to the background (designated as B). The results of this “binning” process were exported into an Excel spreadsheet.

The lignified area within an image taken at 50× magnification was semi-quantified and represented as the ratio (R) of the lignified region relative to the whole tissue within an image. The R value was calculated as follows: R=X/(X+NL). The R values from tissue sections of three plants per transformation event were averaged, and the standard deviation was calculated for each average R value. The average R value and standard deviation for each transformation event was compared to the average R value and standard deviation for the wild-type plants to determine whether the difference between the average R values was statistically significant.

The degree of increase or decrease in lignin content within the sampled stem sections of a transgenic line relative to the lignin content in sampled stem sections of wild-type plants was calculated using the following formula.

[(R_(transgenic))−(Average R_(Wild-type))]/(Average R_(Wild-type))×100

A relative value, calculated using the formula above, that was positive indicated an increased lignin content in the transgenic line relative to wild-type plants (Table 7). A relative value that was negative indicated a decreased lignin content in the transgenic line relative to wild-type plants (Table 7).

The microscope images of stem tissue sections were also qualitatively inspected to determine if there was ectopic deposition of lignin in regions not normally lignified in wild-type stem tissues, or if there were developmental changes in tissue arrangement compared to the arrangement in wild-type plants.

Digital images of seedlings and whole leaf tissues were taken in jpeg format using an Epson 4870 Photo Scanner. Images of transgenic tissues were compared to images of wild-type tissues to qualitatively determine if there was ectopic or increased accumulation of lignin in organs from transgenic plants as compared to organs from wild-type plants.

Results of Histological Analysis

Results of the semi-quantitative analysis of the lignified areas of stem sections from wild-type Arabidopsis plants at different developmental stages are summarized in Table 6.

TABLE 6 Lignin content of wild-type Arabidopsis plants at different stages of development Development Stage (Days after Stem R value Standard Germination) Region (Average) Deviation Comments 18 Top N/A Tissues too soft for sectioning Middle 0.03 Tissues still soft for sectioning Base 0.06 Tissues still soft for sectioning 24 Top N/A Tissues too soft for sectioning Middle 0.25 0.04 Base 0.30 0.06 25 Top N/A Tissues too soft for sectioning Middle N/A Base 0.29 0.03 27 Top 0.17 Tissues still soft for sectioning Middle 0.23 0.03 Base 0.32 0.10 35 Top 0.23 0.08 Middle 0.21 0.005 Base 0.37 0.09 Stem becoming brittle

Based on the results presented in Table 6, the basal regions of transgenic and corresponding wild-type control plants between 24 to 26 days post germination were used for histological analysis. The results are summarized in Table 7.

TABLE 7 Summary of the histological analysis of lignin content in transgenic Arabidopsis lines Change in Gemini ID lignin content or relative to Genomic Transgenic line - wild-type Locus Source Construct Code event controls Observable Phenotype 538F5 Zm Clone ID 331755 ME10647-02 30% Increase ME10647-03 34% Increase 552A6 Zm Clone ID 240112 ME08450-01 35% Increase ME08450-05 35% Increase 553H6 Gm Clone ID 691319 ME05057-01 73% Decrease Dwarf; twisted rosette leaves; “wilting” under greenhouse conditions ME05057-05 56% Decrease Dwarf; twisted rosette leaves; “wilting” under greenhouse conditions ME05057-06 39% Decrease Dwarf; twisted rosette leaves; “wilting” under greenhouse conditions ME05057-07 35% Decrease Dwarf; twisted rosette leaves; “wilting” under greenhouse conditions 5217H1 Pt Gemini ID 5217H1 ME23571-01 Increase Dwarf; vascular bundles of amphivasal type ME23571-03 25% Increase Dwarf; vascular bundles of amphivasal type ME23571-04 28% Increase Shorter than wild-type; vascular bundles of amphivasal type At1g05710 At Clone ID 3900 ME03301-02 50% Decrease Shorter than wild-type ME03301-05 36% Decrease Shorter than wild-type ME03301-06 19% Decrease Shorter than wild-type At1g15100 At Clone ID 5398 ME02276-03 22% Increase ME02276-04 23% Increase ME02276-05 28% Increase At1g16490 At Clone ID 152630 ME02500-03 38% Increase ME02500-05 21% Increase At1g25560 At Clone ID 38311 ME01567-02 35% Decrease Shorter than wild-type ME01567-04 15% Decrease At1g54830 At Clone ID 36272 ME01535-02 27% Increase ME01535-03 24% Increase ME01535-04 26% Increase ME01535-05 31% Increase At1g74840 At Clone ID 117643 ME00122-01 16% Increase ME00122-02 20% Increase ME00122-03 17% Increase ME00122-04 25% Increase At2g05440 At Clone ID 113443 ME02171-01 41% Increase ME02171-02 29% Increase ME02171-04 18% Increase Clone ID 207629 ME02589-02 Increase Ectopic lignin in seedling petiole ME02589-04 16% Increase Ectopic lignin in seedling petiole ME02589-05 Increase Ectopic lignin in seedling petiole Clone ID 118184 ME12975-01 26% Increase ME12975-04 25% Increase ME12975-05 25% Increase At3g20310 At Clone ID 124720 ME04445-03 Increase Low ectopic lignin in pith ME04445-04 33% Increase Ectopic lignin in pith; reduced fertility ME04445-05 38% Increase Ectopic lignin in pith; reduced fertility At3g52380 At Clone ID 14246 ME03502-05 15% Increase Amphivasal vascular bundle; extended xylem region At4g09960 At Clone ID 32791 ME01486-02 34% Decrease Smaller, shorter than wild- type ME01486-07 36% Decrease Smaller, shorter than wild- type ME01486-08 45% Decrease Smaller, shorter than wild- type At4g17500 At Clone ID 6042 ME02013-02 33% Increase ME02013-03 16% Increase ME02013-05 30% Increase Low ectopic lignin in pith At4g35570 At Clone ID 16204 ME22388-02 16% Decrease Curly rosette leaves ME22388-05 14% Decrease ME22388-06 12% Decrease Curly rosette leaves At4g39260 At Clone ID 97001 ME04442-02 10% Increase ME04442-03 13% Increase Clone ID 1003205 ME04932-01 20% Increase ME04932-05  6% Increase At5g02590 At Clone ID 13930 ME06485-03 58% Increase ME06485-05 84% Increase At5g25220 At Clone ID 21240 ME06492-02 42% Decrease Shorter than wild-type ME06492-07 29% Decrease Shorter than wild-type At5g61600 At Clone ID 92102 ME04024-01 38% Increase Low ectopic lignin in the pith; amphivasal vascular bundle Zm = Zea mays; Gm = Glycine max; Pt = Populus trichocarpa; At = Arabidopsis thaliana

Clone ID 1003205, listed in Table 7 above, is a homolog of Clone ID 266712, listed in Table 4 above. Clone ID 97001 is a different polypeptide encoded by genomic locus At4g39260 that also has activity based on histology data (Table 7). In addition, a homolog of Clone ID 1003205, identified herein as Clone ID 1011900 (SEQ ID NO:193), is associated with a p-Coumarate 3-hydroxylase regulatory region.

Ectopic deposition of lignin was observed in the pith (the central parenchyma region of the stem) in some of the transgenic lines exhibiting increased lignin accumulation, such as ME02013, ME04024, and ME04445 (FIG. 52, panels A-E). The extent of lignin deposition in the pith was much higher in ME04445.

The transgenic line ME03502 was observed to have an increased accumulation of lignin and a vascular bundle arrangement that was altered from a collateral type to an amphivasal type (FIG. 52, panels F-G). A collateral type is typical of a wild-type arrangement, where the phloem cells are surrounded by cortex cells towards the epidermal tissues and by xylem cells towards the pith. In an amphivasal type of arrangement, the phloem tissues are surrounded by xylem cells. It appeared that some of the cortical cells were converted to lignified xylem cells in plants from ME03502.

Some transgenic lines such as ME03301 and ME05057 were observed to have a decreased accumulation of lignin relative to wild-type plants and a reduced height. The transgenic line ME22388 was observed to have a decreased accumulation of lignin relative to wild-type plants, but did not exhibit a reduced height. The cylindrical band corresponding to the xylem-interfascicular region was thinner in the transgenic line ME03301 than that which is normally observed in wild-type plants at the time the tissue sections were sampled. In the case of transgenic line ME05057, the xylem-interfascicular region was not fully developed at the time of sampling.

Two transgenic lines, ME04442 and ME04932, that were observed to have an increased lignin content (Table 7) were each transformed with a nucleic acid encoding a polypeptide homolog of the regulatory protein identified herein as Gemini ID 531F2 (SEQ ID NO:1860), which was identified as being associated with the 4CL and F5H1 regulatory regions (Table 4).

Example 4 Determination of Functional Homolog and/or Ortholog Sequences

A candidate sequence was considered a functional homolog or ortholog of a reference sequence if the candidate and reference sequences encoded proteins having a similar function and/or activity. A process known as Reciprocal BLAST (Rivera et al., Proc. Natl. Acad. Sci. USA, 95:6239-6244 (1998)) was used to identify potential functional homolog and/or ortholog sequences from databases consisting of all available public and proprietary peptide sequences, including NR from NCBI and peptide translations from Ceres clones.

Before starting a Reciprocal BLAST process, a specific reference polypeptide was searched against all peptides from its source species using BLAST in order to identify polypeptides having BLAST sequence identity of 80% or greater to the reference polypeptide and an alignment length of 85% or greater along the shorter sequence in the alignment. The reference polypeptide and any of the aforementioned identified polypeptides were designated as a cluster.

The BLASTP version 2.0 program from Washington University at Saint Louis, Mo., USA was used to determine BLAST sequence identity and E-value. The BLASTP version 2.0 program includes the following parameters: 1) an E-value cutoff of 1.0e-5; 2) a word size of 5; and 3) the -postsw option. The BLAST sequence identity was calculated based on the alignment of the first BLAST HSP (High-scoring Segment Pairs) of the identified potential functional homolog and/or ortholog sequence with a specific reference polypeptide. The number of identically matched residues in the BLAST HSP alignment was divided by the HSP length, and then multiplied by 100 to get the BLAST sequence identity. The HSP length typically included gaps in the alignment, but in some cases gaps were excluded.

The main Reciprocal BLAST process consists of two rounds of BLAST searches; forward search and reverse search. In the forward search step, a reference polypeptide sequence, “polypeptide A,” from source species SA was BLASTed against all protein sequences from a species of interest. Top hits were determined using an E-value cutoff of 10⁻⁵ and a sequence identity cutoff of 35%. Among the top hits, the sequence having the lowest E-value was designated as the best hit, and considered a potential functional homolog or ortholog. Any other top hit that had a sequence identity of 80% or greater to the best hit or to the original reference polypeptide was considered a potential functional homolog or ortholog as well. This process was repeated for all species of interest. In the reverse search round, the top hits identified in the forward search from all species were BLASTed against all protein sequences from the source species SA. A top hit from the forward search that returned a polypeptide from the aforementioned cluster as its best hit was also considered as a potential functional homolog or ortholog.

Functional homologs and/or orthologs were identified by manual inspection of potential functional homolog and/or ortholog sequences. Representative functional homologs and/or orthologs and their corresponding reference sequences are shown in FIGS. 1-51 and FIGS. 53-131. Some of the homologs and/or orthologs identified using Reciprocal BLAST were analyzed for association with various regulatory regions as described in Example 2 above. The results are presented in Table 8.

TABLE 8 Combinations of regulatory regions and regulatory proteins, or corresponding homologs/orthologs, producing expression of a reporter gene operably linked to each regulatory region Regulatory Associated Associated Region Tested Regulatory Regulatory Homolog/ for Association Protein Region Ortholog with Homolog/ Luciferase SEQ ID NO: SEQ ID NO: SEQ ID NO: Ortholog Activity Clone 16204 Pt4CL Clone 98140 Pt4CL positive SEQ ID SEQ ID NO: 1909 SEQ ID SEQ ID NO: 1909 NO: 1444 NO: 1445 Clone 16204 PtCCR1 Clone 98140 PtCCR1 negative SEQ ID SEQ ID NO: 1918 SEQ ID SEQ ID NO: 1918 NO: 1444 NO: 1445 Clone 560731 PtCCR1 Clone 4267 PtCCR1 negative SEQ ID SEQ ID NO: 1918 SEQ ID SEQ ID NO: 1918 NO: 1628 NO: 1633 Clone 560731 PtPAL4 Clone 4267 PtPAL4 positive SEQ ID SEQ ID NO: 1910 SEQ ID SEQ ID NO: 1910 NO: 1628 NO: 1633 Clone 156298 PtF5H1 Clone 398632 PtF5H1 negative SEQ ID NO: 490 SEQ ID NO: 1912 SEQ ID NO: 502 SEQ ID NO: 1912 Clone 2942 Pt4CL Clone 337432 Pt4CL negative SEQ ID NO: 671 SEQ ID NO: 1909 SEQ ID NO: 676 SEQ ID NO: 1909 Clone 2942 PtPAL4 Clone 337432 PtPAL4 negative SEQ ID NO: 671 SEQ ID NO: 1910 SEQ ID NO: 676 SEQ ID NO: 1910 Clone 6397 PtCCR1 Clone 605218 PtCCR1 negative SEQ ID SEQ ID NO: 1918 SEQ ID SEQ ID NO: 1918 NO: 1637 NO: 1639 Clone 603410 PtCCR1 positive SEQ ID SEQ ID NO: 1918 NO: 1752 Clone 6397 PtPAL4 Clone 605218 PtPAL4 negative SEQ ID SEQ ID NO: 1910 SEQ ID SEQ ID NO: 1910 NO: 1637 NO: 1639 Clone 603410 PtPAL4 negative SEQ ID SEQ ID NO: 1910 NO: 1752 Clone 603410 PtC4H Clone 6397 PtC4H negative SEQ ID SEQ ID NO: 1916 SEQ ID SEQ ID NO: 1916 NO: 1752 NO: 1637 Clone 605218 PtC4H negative SEQ ID SEQ ID NO: 1916 NO: 1639 Clone 38311 PtF5H1 Clone 597624 PtF5H1 positive SEQ ID SEQ ID NO: 1912 SEQ ID SEQ ID NO: 1912 NO: 1285 NO: 1289 Clone 19561 PtF5H1 negative SEQ ID SEQ ID NO: 1912 NO: 1957 Clone 519 PtC4H Clone 560948 PtC4H negative SEQ ID SEQ ID NO: 1916 SEQ ID SEQ ID NO: 1916 NO: 1806 NO: 1817 Clone 560681 PtC4H negative SEQ ID SEQ ID NO: 1916 NO: 1815 Clone 519 PtCCR1 Clone 560948 PtCCR1 negative SEQ ID SEQ ID NO: 1918 SEQ ID SEQ ID NO: 1918 NO: 1806 NO: 1817 Clone 560681 PtCCR1 negative SEQ ID SEQ ID NO: 1918 NO: 1815 Clone 519 PtF5H1 Clone 560948 PtF5H1 negative SEQ ID SEQ ID NO: 1912 SEQ ID SEQ ID NO: 1912 NO: 1806 NO: 1817 Clone 560681 PtF5H1 negative SEQ ID SEQ ID NO: 1912 NO: 1815 Clone 519 PtPAL4 Clone 560948 PtPAL4 positive SEQ ID SEQ ID NO: 1910 SEQ ID SEQ ID NO: 1910 NO: 1806 NO: 1817 Clone 560681 PtPAL4 positive SEQ ID SEQ ID NO: 1910 NO: 1815 Clone 8607 PtCAD6 Clone 560948 PtCAD6 negative SEQ ID SEQ ID NO: 1915 SEQ ID SEQ ID NO: 1915 NO: 1785 NO: 1817 Clone 560681 PtCAD6 negative SEQ ID SEQ ID NO: 1915 NO: 1815 Clone 8607 PtCCoAOMT Clone 560948 PtCCoAOMT negative SEQ ID SEQ ID NO: 1914 SEQ ID SEQ ID NO: 1914 NO: 1785 NO: 1817 Clone 560681 PtCCoAOMT negative SEQ ID SEQ ID NO: 1914 NO: 1815 Clone 8607 PtF5H1 Clone 560948 PtF5H1 negative SEQ ID SEQ ID NO: 1912 SEQ ID SEQ ID NO: 1912 NO: 1785 NO: 1817 Clone 560681 PtF5H1 negative SEQ ID SEQ ID NO: 1912 NO: 1815 Clone 8607 PtPAL4 Clone 560948 PtPAL4 positive SEQ ID SEQ ID NO: 1910 SEQ ID SEQ ID NO: 1910 NO: 1785 NO: 1817 Clone 560681 PtPAL4 positive SEQ ID SEQ ID NO: 1910 NO: 1815 Clone 124720 PtF5H1 Clone 1044385 PtF5H1 negative SEQ ID SEQ ID NO: 1912 SEQ ID SEQ ID NO: 1912 NO: 1302 NO: 1304 Clone 124720 PtPAL4 Clone 1044385 PtPAL4 negative SEQ ID SEQ ID NO: 1910 SEQ ID SEQ ID NO: 1910 NO: 1302 NO: 1304 Clone 8334 PtCCoAOMT Clone 114858 PtCCoAOMT negative SEQ ID SEQ ID NO: 1914 SEQ ID SEQ ID NO: 1914 NO: 1104 NO: 1106 Clone 8334 PtPAL4 Clone 114858 PtPAL4 negative SEQ ID SEQ ID NO: 1910 SEQ ID SEQ ID NO: 1910 NO: 1104 NO: 1106 Clone 543118 PtCCR1 Clone 10506 PtCCR1 negative SEQ ID NO: 994 SEQ ID NO: 1918 SEQ ID SEQ ID NO: 1918 NO: 1047 Clone 3115 PtCCR1 positive SEQ ID SEQ ID NO: 1918 NO: 1045 Clone 115366 PtCCR1 Clone 148506 PtCCR1 negative SEQ ID NO: 381 SEQ ID NO: 1918 SEQ ID NO: 385 SEQ ID NO: 1918 Clone 115366 PtPAL4 Clone 148506 PtPAL4 negative SEQ ID NO: 381 SEQ ID NO: 1910 SEQ ID NO: 385 SEQ ID NO: 1910 Clone 3929* PtF5H1 Clone 207629* PtF5H1 positive SEQ ID SEQ ID NO: 1912 SEQ ID SEQ ID NO: 1912 NO: 1185 NO: 1192 Clone 18215 PtF5H1 negative SEQ ID SEQ ID NO: 1912 NO: 1188 Clone 3929 PtPAL4 Clone 207629 PtPAL4 negative SEQ ID SEQ ID NO: 1910 SEQ ID SEQ ID NO: 1910 NO: 1185 NO: 1192 Clone 18215 PtPAL4 negative SEQ ID SEQ ID NO: 1910 NO: 1188 *Indicates that the regulatory protein also was observed to be associated with the indicated regulatory region in a secondary screen in Populus, described in Example 2. Pt4CL = Populus 4-Coumaroyl:CoA ligase PtF5H1 = Populus Ferulate 5-hydroxylase PtCCR1 = Populus Cinnamoyl-CoA reductase PtC4H = Populus Cinnamate 4-hydroxylase PtPAL4 = Populus Phenylalanine ammonia lyase PtCAD6 = Populus Cinnamyl alcohol dehydrogenase PtCCoAOMT = Populus Caffeoyl-CoA O-methyltransferase

Clone 19561 (SEQ ID NO:1957), which is a homolog/ortholog of Clone 38311 (SEQ ID NO:1285), also was observed to associate with regulatory region PtCCR1 (SEQ ID NO:1918).

Example 5 Analysis of Lignin Structure and Content in Transgenic Arabidopsis Lines

Arabidopsis overexpression lines (ME lines) were grown in batches in the greenhouse under long-day condition at 28° C. until senescence stage. Each transformation event corresponding to an overexpression line was planted in several pots (represented as replicates) with each pot randomly distributed in separate flats. The corresponding wild type non-transgenic control for each batch was planted in the same manner. At the senescence stage, stem tissues were divided into three parts (bottom, center, and upper) and were collected separately. Collected tissues were dried in a freeze dryer for at least two days before milling.

Pyrolysis GC-MS was performed on a Py-2020 is pyrolyzer (Frontier Labs, Japan) coupled to a QP2010 GC-MS (Shimadzu, Japan). Finely ground material (2 mm minimum) was weighed out (3 mg) into a deactivated stainless steel cup. Sample was introduced into the pyrolyzer set at 500° C. by gravity. The interface between the pyrolyzer and GC inlet was set at 300° C. Separation of pyrolysates was performed on a GC-column (VF-5MS, 30M×0.25 mm×0.25 um). Helium flow through the pyrolyzer and column was set at 1052 mL/min and 1.0 mL/min respectively. Inlet split ratio was 700:1. Column temperature program was initially set at 70° C. (held for 4 minutes) at a ramp rate of 20° C./min to a final temperature of 350° C. Mass spectral acquisition was at 3333 amu/sec from 50 amu-300 amu after a 4.5 min delay.

The areas of the peaks corresponding to different types of lignin monomers (i.e., H=p-Hydroxyphenyl monomer, G=Guaiacyl monomer, S=Syringyl monomer) and to levoglucosan and furfural (both as cellulose markers) were collected. Total lignin is the sum of all the peaks for H, G, and S monomers. The ratios shown in Table 9 were normalized relative to total lignin.

Comparisons of overexpression lines were made relative to the wild-type control for each batch. The overexpression of the following clones or genes (as indicated by Annot IDs) leads to relatively higher S/G ratio (generally indicative of a positive parameter that may enhance conversion of biomass to ethanol) as shown by their corresponding ME lines: 124720 (ME04445), 6042 (ME02013), Annot 1493072 (ME23571), 38915 (ME01050), 108109 (ME01973), 92102 (ME04024), 5398 (ME02276), 108362 (ME03210), 603410 (ME03986), Annot 550729 (ME10852), Annot 548715 (ME11894), Annot 554970 (ME10196), 41875 (ME04890), 34589 (ME05722 and ME01130), Annot 535161 (ME05335), 38360 (ME04274), 1821051 (ME27373), 11988 (ME00259), 2898 (ME05855), Annot 869854 (ME18127), Annot 869790 (ME20794).

The overexpression of clone 208429 in ME12091 line leads to lower S/G ratio indicating that downregulating the corresponding gene (by antisense or RNAi) may reverse this effect.

The overexpression of clones 1804242 (ME26515) and 1821051 (ME27373) leads to an increase in cellulose/lignin ratio indicating an increase in the absolute amount of cellulose or a decrease in lignin.

The overexpression of the following clones leads to lower cellulose/lignin ratio (indicating either an increase in the absolute amount of lignin or decrease in cellulose) as shown by their corresponding ME lines: 11988 (ME00259), 8049 (ME01752), 2898 (ME05855), 118184 (ME12975), 34589 (ME01130), 11830 (ME03582), 20948 (ME06540).

TABLE 9 Amount SEQ H/Total G/Total S/Total of Clone or ID Transformation Lignin Lignin Lignin S/G H/G Cellulose/ Batch AnnotID NO Events Ratio Ratio Ratio Ratio Ratio Lignin 1 Ceres 1423 ME03502-01-B 0.13 0.63 0.24 0.39 0.20 Clone ID 14246 1 ME03502-05-C 0.13 0.62 0.24 0.39 0.21 1 Ceres 1302 ME04445-04-B 0.13 0.62 0.25 0.40 0.21 Clone ID 124720 1 ME04445-05-A 0.11 0.62 0.27 0.44 0.18 1 Ceres 1892 ME23571-01-B 0.11 0.62 0.26 0.42 0.18 Annot ID 1493072 1 ME23571-03-A 0.12 0.62 0.25 0.41 0.19 1 Ceres 1064 ME02013-01- 0.11 0.62 0.26 0.42 0.18 Clone 01-C ID 6042 1 ME02013-05- 0.14 0.59 0.25 0.42 0.24 01-E 1 Ceres 1692 ME04024-01-A 0.14 0.62 0.23 0.38 0.22 Clone ID 92102 1 ME04024-01-B 0.14 0.64 0.21 0.32 0.22 1 ME04024-05-E 0.12 0.60 0.27 0.45 0.21 1 Ceres 1897 ME02276-03-A 0.17 0.58 0.24 0.42 0.29 Clone ID 5398 1 ME02276-04-D 0.13 0.60 0.26 0.44 0.22 1 ME02276-05-B 0.14 0.61 0.25 0.40 0.22 1 Ceres 1192 ME02589-04-D 0.12 0.62 0.26 0.42 0.19 Clone ID 207629 1 Wild WT 0.10 0.64 0.25 0.39 0.16 Type Control 2 Ceres 2087 ME06884-01-C 0.12 0.65 0.24 0.36 0.18 0.10 Clone ID 28026 2 ME06884-05-F 0.16 0.61 0.23 0.38 0.26 0.10 2 Ceres 1383 ME07070-01-E 0.15 0.62 0.24 0.38 0.24 0.10 Clone ID 115924 2 ME07070-03-G 0.14 0.61 0.25 0.42 0.23 0.10 2 Ceres 381 ME07290-02-D 0.17 0.59 0.25 0.42 0.28 0.08 Clone ID 115366 2 ME07290-05-A 0.14 0.63 0.23 0.36 0.23 0.10 2 Ceres 170 ME11448-01-G 0.13 0.61 0.26 0.42 0.21 0.11 Annot ID 844490 2 ME11448-03-C 0.14 0.62 0.23 0.37 0.23 0.10 2 Ceres 610 ME07556-04-D 0.17 0.61 0.21 0.35 0.28 0.09 Clone ID 25816 2 ME07556-05-D 0.14 0.61 0.25 0.42 0.23 0.10 2 Ceres 548 ME03547-01-D 0.13 0.60 0.27 0.45 0.21 0.09 Clone ID 1845 2 ME03547-05-A 0.14 0.58 0.27 0.47 0.25 0.10 2 Ceres 707 ME10647-02-E 0.14 0.58 0.28 0.48 0.23 0.09 Clone ID 331755 2 ME10647-03-A 0.13 0.67 0.20 0.30 0.19 0.09 2 Ceres 1752 ME03986-03-G 0.16 0.56 0.28 0.50 0.29 0.11 Clone ID 603410 2 ME03986-05-G 0.16 0.52 0.32 0.60 0.30 0.13 2 Ceres 370 ME07113-03 0.14 0.60 0.26 0.44 0.23 0.10 Clone ID 112194 2 ME07113-05 0.14 0.61 0.25 0.40 0.23 0.10 2 Ceres 1315 ME12091-01 0.17 0.61 0.22 0.36 0.27 0.10 Clone ID 208429 2 ME07113-02 0.13 0.64 0.23 0.36 0.20 0.08 2 Wild WT 0.15 0.59 0.26 0.44 0.25 0.10 Type Control 3 Ceres 1892 ME23571-01-A 0.13 0.60 0.27 0.44 0.22 0.11 Annot ID 1493072 3 ME23571-03-B 0.13 0.57 0.30 0.53 0.23 0.12 3 ME23571-04-B 0.14 0.59 0.27 0.46 0.23 0.10 3 Ceres 1573 ME01535-02-B 0.13 0.60 0.27 0.45 0.22 0.10 Clone ID 36272 3 ME01535-05-C 0.14 0.61 0.26 0.42 0.22 0.12 3 Ceres 1876 ME08968-01-A 0.14 0.61 0.25 0.42 0.22 0.11 Clone ID 520515 3 ME08968-04-A 0.14 0.59 0.27 0.45 0.23 0.11 3 Ceres 1564 ME12097-01-A 0.14 0.60 0.26 0.44 0.23 0.10 Clone ID 333416 3 ME12097-05-A 0.14 0.60 0.27 0.44 0.23 0.09 3 Wild WT 0.15 0.56 0.28 0.50 0.27 0.12 Type Control 4 Ceres 652 ME05855-02 0.14 0.61 0.25 0.41 0.22 0.15 Clone ID 2898 4 ME05855-03 0.09 0.71 0.20 0.29 0.13 0.04 4 Ceres 96 ME12380-01-H 0.10 0.69 0.22 0.31 0.14 0.09 Annot ID 541887 4 Ceres 601 ME08450-01-B 0.10 0.68 0.22 0.33 0.15 0.09 Clone ID 240112 4 ME08450-05-A 0.09 0.69 0.22 0.32 0.13 0.09 4 Wild WT 0.10 0.68 0.22 0.32 0.15 0.09 Type Control 5 Ceres 1393 ME12975-01-A 0.11 0.68 0.21 0.30 0.16 0.08 Clone and ID 1201 118184 5 ME12975-04-A 0.10 0.69 0.21 0.30 0.15 0.09 5 Ceres 555 ME07579-01- 0.11 0.69 0.21 0.30 0.16 0.11 Clone 99-F ID 205648 5 ME07579-03- 0.12 0.68 0.20 0.30 0.17 0.10 99-B 5 Ceres 134 ME10852-03-A 0.15 0.64 0.21 0.33 0.24 0.10 Annot ID 550729 5 ME10852-05-A 0.14 0.61 0.25 0.42 0.23 0.14 5 Ceres 106 ME11894-01-B 0.14 0.60 0.25 0.42 0.24 0.11 Annot ID 548715 5 ME11894-05-C 0.14 0.63 0.23 0.37 0.22 0.14 5 Ceres 149 ME10196-01-E 0.14 0.60 0.26 0.44 0.24 0.12 Annot ID 554970 5 ME10196-02-C 0.13 0.63 0.24 0.38 0.20 0.13 5 Ceres 898 ME04890-02-C 0.14 0.61 0.25 0.41 0.23 0.14 Clone ID 41875 5 ME04890-03-F 0.14 0.58 0.27 0.47 0.25 0.14 5 Ceres 1570 ME05722-01-A 0.14 0.58 0.28 0.48 0.25 0.15 Clone ID 34589 5 ME05722-08-A 0.13 0.61 0.26 0.43 0.22 0.11 5 Ceres 1570 ME01130-01-A 0.16 0.56 0.27 0.49 0.29 0.03 Clone ID 34589 5 ME01130-03- 0.13 0.66 0.22 0.33 0.19 0.10 99-A 5 Wild WT 0.11 0.69 0.20 0.29 0.17 0.12 Type Control 6 Ceres 520 ME01404-03-B 0.14 0.64 0.22 0.35 0.21 0.13 Clone ID 158240 6 ME01404-05-C 0.12 0.64 0.24 0.37 0.19 0.13 6 Ceres 1637 ME02011-04-A 0.13 0.62 0.25 0.40 0.21 0.12 Clone and ID 6397 1755 6 ME02011-05-A 0.14 0.63 0.24 0.38 0.22 0.11 6 Ceres 781 ME04213-02- 0.11 0.65 0.24 0.37 0.17 0.11 Clone 99-E ID 40729 6 ME04213-04- 0.12 0.65 0.23 0.35 0.18 0.12 99-D 6 Ceres 1840 ME04241-04-B 0.15 0.64 0.20 0.31 0.24 0.12 Clone ID 14432 6 ME04241-05-D 0.17 0.64 0.19 0.30 0.27 0.13 6 Ceres 816 ME04274-01-F 0.13 0.59 0.28 0.47 0.23 0.11 Clone ID 38360 6 Ceres 1830 ME05105-01-B 0.12 0.63 0.25 0.40 0.20 0.11 Clone ID 100085 6 ME05105-03- 0.14 0.62 0.24 0.38 0.22 0.10 99-B 6 Ceres 1211 ME15117-01-C 0.12 0.64 0.24 0.37 0.18 0.13 Clone ID 14909 6 ME15117-05-A 0.14 0.63 0.23 0.37 0.23 0.14 6 Ceres 1444 ME22388-02-B 0.24 0.58 0.18 0.30 0.41 0.10 Clone ID 16204 6 Wild WT 0.12 0.64 0.24 0.38 0.19 0.11 Type Control

Example 6 Determination of Functional Homologs by Hidden Markov Models

Hidden Markov Models (HMMs) were generated by the program HMMER 2.3.2. To generate each HMM, the default HMMER 2.3.2 program parameters, configured for glocal alignments, were used.

An HMM was generated using the sequences shown in FIG. 28 as input. These sequences were fitted to the model and a representative HMM bit score for each sequence is shown in the Sequence Listing. Additional sequences were fitted to the model, and representative HMM bit scores for any such additional sequences are shown in the Sequence Listing. The results indicate that these additional sequences are functional homologs of SEQ ID NO:566.

The procedure above was repeated and an HMM was generated for each group of sequences shown in FIGS. 30, 53, 74, 81, 107, and 119, using the sequences shown in each Figure as input for that HMM. A representative bit score for each sequence is shown in the Sequence Listing. Additional sequences were fitted to certain HMMs, and representative HMM bit scores for such additional sequences are shown in the Sequence Listing. The results indicate that these additional sequences are functional homologs of the sequences used to generate that HMM.

Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

1.-3. (canceled)
 4. A plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide, wherein the HMM bit score of the amino acid sequence of said polypeptide is greater than about 20, said HMM based on the amino acid sequences depicted in one of FIG. 1-51 or 53-131, and wherein a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.
 5. A plant cell comprising an exogenous nucleic acid, said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence encoding a polypeptide having 80% or greater sequence identity to a polypeptide sequence selected from the group consisting of SEQ ID NO:96, SEQ ID NOs:98-100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NOs:110-112, SEQ ID NOs:114-117, SEQ ID NOs:119-122, SEQ ID NO:124, SEQ ID NOs:126-128, SEQ ID NOs:130-132, SEQ ID NOs:134-137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:143, SEQ ID NOs:145-147, SEQ ID NO:149, SEQ ID NOs:151-155, SEQ ID NO:157, SEQ ID NO:159, SEQ ID NO:161, SEQ ID NO:163, SEQ ID NOs:165-168, SEQ ID NO:170, SEQ ID NOs:172-176, SEQ ID NOs:178-194, SEQ ID NO:196, SEQ ID NOs:198-215, SEQ ID NO:217, SEQ ID NO:219, SEQ ID NOs:221-251, SEQ ID NO:253, SEQ ID NOs:255-256, SEQ ID NO:258, SEQ ID NO:260, SEQ ID NOs:262-265, SEQ ID NO:267, SEQ ID NOs:269-270, SEQ ID NOs:272-273, SEQ ID NOs:275-277, SEQ ID NOs:279-280, SEQ ID NO:282, SEQ ID NO:284, SEQ ID NOs:286-287, SEQ ID NOs:289-290, SEQ ID NO:292, SEQ ID NOs:294-298, SEQ ID NO:300, SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NOs:308-313, SEQ ID NOs:315-316, SEQ ID NOs:318-319, SEQ ID NO:321, SEQ ID NO:323, SEQ ID NOs:325-326, SEQ ID NO:328, SEQ ID NO:330, SEQ ID NO:332, SEQ ID NOs:334-335, SEQ ID NO:337, SEQ ID NO:339-341, SEQ ID NO:343, SEQ ID NO:345, SEQ ID NO:347-351, SEQ ID NO:353, SEQ ID NO:355, SEQ ID NO:357-359, SEQ ID NOs:361-368, SEQ ID NO:370, SEQ ID NO:372, SEQ ID NOs:374-375, SEQ ID NO:377, SEQ ID NO:379, SEQ ID NOs:381-385, SEQ ID NOs:387-389, SEQ ID NOs:391-392, SEQ ID NOs:394-398, SEQ ID NO:400, SEQ ID NOs:402-403, SEQ ID NO:405, SEQ ID NO:407, SEQ ID NO:409, SEQ ID NO:411, SEQ ID NO:413, SEQ ID NO:415, SEQ ID NOs:417-430, SEQ ID NOs:432-434, SEQ ID NO:436, SEQ ID NO:438, SEQ ID NO:440, SEQ ID NOs:442-443, SEQ ID NOs:445-447, SEQ ID NO:449, SEQ ID NOs:451-452, SEQ ID NOs:454-457, SEQ ID NO:459, SEQ ID NOs:461-463, SEQ ID NOs:465-468, SEQ ID NOs:470-471, SEQ ID NO:473, SEQ ID NOs:475-476, SEQ ID NOs:478-481, SEQ ID NOs:483-485, SEQ ID NOs:487-488, SEQ ID NO:490, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NOs:496-499, SEQ ID NOs:501-502, SEQ ID NOs:504-506, SEQ ID NO:508, SEQ ID NOs:510-514, SEQ ID NO:516, SEQ ID NO:518, SEQ ID NOs:520-522, SEQ ID NO:524, SEQ ID NOs:526-527, SEQ ID NOs:529-533, SEQ ID NO:535, SEQ ID NO:537, SEQ ID NO:539, SEQ ID NO:541, SEQ ID NO:543, SEQ ID NOs:545-546, SEQ ID NOs:548-551, SEQ ID NO:553, SEQ ID NOs:555-561, SEQ ID NOs:563-564, SEQ ID NOs:566-568, SEQ ID NO:570, SEQ ID NO:572, SEQ ID NOs:574-576, SEQ ID NOs:578-579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NOs:585-588, SEQ ID NOs:590-591, SEQ ID NOs:593-594, SEQ ID NOs:596-597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NOs:603-604, SEQ ID NO:606, SEQ ID NO:608, SEQ ID NO:610, SEQ ID NO:612, SEQ ID NOs:614-617, SEQ ID NO:619, SEQ ID NOs:621-636, SEQ ID NOs:638-648, SEQ ID NO:650, SEQ ID NOs:652-654, SEQ ID NOs:656-657, SEQ ID NO:659, SEQ ID NOs:661-663, SEQ ID NOs:665-669, SEQ ID NOs:671-673, SEQ ID NOs:675-676, SEQ ID NO:678, SEQ ID NO:680, SEQ ID NO:682, SEQ ID NO:684, SEQ ID NOs:686-687, SEQ ID NOs:689-693, SEQ ID NOs:695-696, SEQ ID NO:698, SEQ ID NOs:700-701, SEQ ID NO:703, SEQ ID NO:705, SEQ ID NO:707, SEQ ID NOs:709-711, SEQ ID NO:713, SEQ ID NOs:715-716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:722, SEQ ID NOs:724-728, SEQ ID NOs:730-735, SEQ ID NOs:737-740, SEQ ID NO:742, SEQ ID NOs:744-745, SEQ ID NOs:747-751, SEQ ID NO:753, SEQ ID NOs:755-758, SEQ ID NOs:760-763, SEQ ID NOs:765-777, SEQ ID NO:779, SEQ ID NOs:781-784, SEQ ID NOs:786-788, SEQ ID NOs:790-791, SEQ ID NOs:793-794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:800, SEQ ID NOs:802-806, SEQ ID NOs:808-809, SEQ ID NOs:811-812, SEQ ID NO:814, SEQ ID NOs:816-818, SEQ ID NO:820, SEQ ID NO:822, SEQ ID NOs:824-826, SEQ ID NO:828, SEQ ID NOs:830-831, SEQ ID NO:833, SEQ ID NOs:835-836, SEQ ID NOs:838-839, SEQ ID NO:841, SEQ ID NOs:843-847, SEQ ID NOs:849-850, SEQ ID NOs:852-853, SEQ ID NOs:855-857, SEQ ID NO:859, SEQ ID NOs:861-863, SEQ ID NOs:865-866, SEQ ID NOs:868-883, SEQ ID NOs:885-888, SEQ ID NO:890, SEQ ID NO:892, SEQ ID NO:894, SEQ ID NO:896, SEQ ID NO:898, SEQ ID NOs:900-902, SEQ ID NOs:904-905, SEQ ID NOs:907-910, SEQ ID NO:912, SEQ ID NOs:914-915, SEQ ID NO:917, SEQ ID NO:919, SEQ ID NOs:921-925, SEQ ID NO:927, SEQ ID NOs:929-932, SEQ ID NO:934, SEQ ID NO:936, SEQ ID NOs:938-941, SEQ ID NO:943 SEQ ID NOs:945-957, SEQ ID NOs:959-962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NOs:968-971, SEQ ID NO:973, SEQ ID NOs:975-978, SEQ ID NO:980, SEQ ID NOs:982-992, SEQ ID NOs:994-1005, SEQ ID NOs:1007-1009, SEQ ID NOs:1011-1014, SEQ ID NOs:1016-1026, SEQ ID NOs:1028-1029, SEQ ID NOs:1031-1033, SEQ ID NOs:1035-1048, SEQ ID NO:1050, SEQ ID NOs:1052-1053, SEQ ID NOs:1055-1056, SEQ ID NO:1058, SEQ ID NO:1060, SEQ ID NO:1062, SEQ ID NOs:1064-1066, SEQ ID NOs:1068-1069, SEQ ID NOs:1071-1076, SEQ ID NOs:1078-1079, SEQ ID NO:1081, SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NOs:1087-1089, SEQ ID NOs:1091-1092, SEQ ID NO:1094, SEQ ID NO:1096, SEQ ID NOs:1098-1102, SEQ ID NOs:1104-1107, SEQ ID NOs:1109-1115, SEQ ID NOs:1117-1120, SEQ ID NOs:1122-1123, SEQ ID NOs:1125-1127, SEQ ID NO:1129, SEQ ID NOs:1131-1132, SEQ ID NO:1134, SEQ ID NOs:1136-1137, SEQ ID NOs:1139-1141, SEQ ID NOs:1143-1147, SEQ ID NOs:1149-1154, SEQ ID NOs:1156-1157, SEQ ID NO:1159, SEQ ID NO:1161, SEQ ID NO:1163, SEQ ID NOs:1165-1169, SEQ ID NO:1171, SEQ ID NOs:1173-1174, SEQ ID NOs:1176-1181, SEQ ID NO:1183, SEQ ID NOs:1185-1207, SEQ ID NO:1209, SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1217, SEQ ID NO:1219, SEQ ID NO:1221, SEQ ID NO:1223, SEQ ID NOs:1225-1235, SEQ ID NO:1237, SEQ ID NO:1239, SEQ ID NO:1241, SEQ ID NO:1243, SEQ ID NO:1245, SEQ ID NO:1247, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1265, SEQ ID NO:1267, SEQ ID NO:1269, SEQ ID NO:1271, SEQ ID NO:1273, SEQ ID NO:1275, SEQ ID NO:1277, SEQ ID NO:1279, SEQ ID NO:1281, SEQ ID NO:1283, SEQ ID NOs:1285-1290, SEQ ID NO:1292, SEQ ID NO:1294, SEQ ID NO:1296, SEQ ID NO:1298, SEQ ID NO:1300, SEQ ID NOs:1302-1309, SEQ ID NO:1311, SEQ ID NO:1313, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1319, SEQ ID NO:1321, SEQ ID NO:1323, SEQ ID NO:1325, SEQ ID NO:1327, SEQ ID NO:1329, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1335, SEQ ID NO:1337, SEQ ID NO:1339, SEQ ID NO:1341, SEQ ID NO:1343, SEQ ID NO:1345, SEQ ID NO:1347, SEQ ID NO:1349, SEQ ID NO:1351, SEQ ID NO:1353, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1359, SEQ ID NOs:1361-1367, SEQ ID NO:1369, SEQ ID NO:1371, SEQ ID NO:1373, SEQ ID NO:1375, SEQ ID NO:1377, SEQ ID NO:1379, SEQ ID NO:1381, SEQ ID NO:1383, SEQ ID NO:1385, SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1391, SEQ ID NO:1393, SEQ ID NO:1395, SEQ ID NO:1397, SEQ ID NO:1399, SEQ ID NO:1401, SEQ ID NO:1403, SEQ ID NOs:1405-1410, SEQ ID NO:1412, SEQ ID NOs:1414-1415, SEQ ID NO:1417, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NOs:1423-1429, SEQ ID NO:1431, SEQ ID NO:1433, SEQ ID NOs:1436-1442, SEQ ID NOs:1444-1463, SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ ID NO:1475, SEQ ID NO:1477, SEQ ID NO:1479, SEQ ID NO:1481, SEQ ID NO:1483, SEQ ID NO:1485, SEQ ID NOs:1487-1491, SEQ ID NOs:1493-1500, SEQ ID NO:1502, SEQ ID NOs:1504-1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, SEQ ID NO:1524, SEQ ID NO:1526, SEQ ID NOs:1528-1534, SEQ ID NO:1536, SEQ ID NO:1538, SEQ ID NO:1540, SEQ ID NO:1542, SEQ ID NO:1544, SEQ ID NO:1546, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:1554, SEQ ID NO:1556, SEQ ID NO:1558, SEQ ID NO:1560, SEQ ID NO:1562, SEQ ID NO:1564, SEQ ID NO:1566, SEQ ID NO:1568, SEQ ID NOs:1570-1571, SEQ ID NO:1573, SEQ ID NO:1575, SEQ ID NO:1577, SEQ ID NO:1579, SEQ ID NO:1581, SEQ ID NO:1583, SEQ ID NO:1585, SEQ ID NO:1587, SEQ ID NO:1589, SEQ ID NO:1591, SEQ ID NO:1593, SEQ ID NOs:1595-1608, SEQ ID NO:1610, SEQ ID NO:1612, SEQ ID NO:1614, SEQ ID NO:1616, SEQ ID NO:1618, SEQ ID NOs:1620-1622, SEQ ID NO:1624, SEQ ID NO:1626, SEQ ID NO:1628, SEQ ID NO:1630, SEQ ID NOs:1632-1635, SEQ ID NOs:1637-1651, SEQ ID NOs:1653-1655, SEQ ID NO:1657, SEQ ID NO:1659, SEQ ID NO:1661, SEQ ID NO:1663, SEQ ID NO:1665, SEQ ID NO:1667, SEQ ID NO:1669, SEQ ID NO:1671, SEQ ID NO:1673, SEQ ID NOs:1675-1679, SEQ ID NO:1681, SEQ ID NOs:1683-1690, SEQ ID NO:1692, SEQ ID NO:1694, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710; SEQ ID NO:1712, SEQ ID NO:1714, SEQ ID NO:1716, SEQ ID NO:1718, SEQ ID NO:1720, SEQ ID NO:1722, SEQ ID NO:1724, SEQ ID NO:1726, SEQ ID NOs:1728-1731, SEQ ID NO:1733, SEQ ID NOs:1735-1747, SEQ ID NOs:1749-1750, SEQ ID NOs:1752-1765, SEQ ID NOs:1767-1775, SEQ ID NO:1777, SEQ ID NO:1779, SEQ ID NO:1781, SEQ ID NO:1783, SEQ ID NOs:1785-1804, SEQ ID NOs:1806-1820, SEQ ID NO:1822, SEQ ID NO:1824, SEQ ID NO:1826, SEQ ID NO:1828, SEQ ID NO:1830, SEQ ID NO:1832, SEQ ID NO:1834, SEQ ID NO:1836, SEQ ID NO:1838, SEQ ID NO:1840, SEQ ID NO:1842, SEQ ID NO:1844, SEQ ID NO:1846, SEQ ID NO:1848, SEQ ID NO:1850, SEQ ID NO:1852, SEQ ID NO:1854, SEQ ID NO:1856, SEQ ID NO:1858, SEQ ID NO:1860, SEQ ID NO:1862, SEQ ID NO:1864, SEQ ID NO:1866, SEQ ID NO:1868, SEQ ID NO:1870, SEQ ID NO:1872, SEQ ID NO:1874, SEQ ID NO:1876, SEQ ID NO:1878, SEQ ID NO:1880, SEQ ID NO:1882, SEQ ID NO:1884, SEQ ID NO:1886, SEQ ID NO:1888, SEQ ID NO:1890, SEQ ID NOs:1892-1895, SEQ ID NO:1897, SEQ ID NO:1899, SEQ ID NOs:1901-1902, SEQ ID NO:1904, SEQ ID NO:1906, SEQ ID NO:1908, SEQ ID NOs:1921-2059, SEQ ID NO:2061, SEQ ID NO:2063, SEQ ID NOs:2065-2083, SEQ ID NO:2085, SEQ ID NO:2087, SEQ ID NO:2089, SEQ ID NO:2091, SEQ ID NO:2093, SEQ ID NO:2095, SEQ ID NO:2097, SEQ ID NO:2099, SEQ ID NO:2101, SEQ ID NO:2103, SEQ ID NO:2105, SEQ ID NO:2107, SEQ ID NO:2109, SEQ ID NO:2111, SEQ ID NO:2113, SEQ ID NO:2115, SEQ ID NO:2117, SEQ ID NO:2119, SEQ ID NO:2121, SEQ ID NO:2123, SEQ ID NO:2125, SEQ ID NO:2127, SEQ ID NO:2129, SEQ ID NO:2131, SEQ ID NO:2133, SEQ ID NO:2135, SEQ ID NO:2137, SEQ ID NO:2139, SEQ ID NO:2141, SEQ ID NO:2143, SEQ ID NO:2145, SEQ ID NO:2147, SEQ ID NO:2149, SEQ ID NO:2151, SEQ ID NO:2153, SEQ ID NO:2155, SEQ ID NO:2157, SEQ ID NO:2159, SEQ ID NO:2161, SEQ ID NO:2162, SEQ ID NO:2164, SEQ ID NO:2166, SEQ ID NO:6168, SEQ ID NO:2170, SEQ ID NO:2172, SEQ ID NO:2174, SEQ ID NO:2176, SEQ ID NO:2178, SEQ ID NO:2180, SEQ ID NO:2182, SEQ ID NO:2184, SEQ ID NO:2186, SEQ ID NO:2188, SEQ ID NO:2190, SEQ ID NO:2192, SEQ ID NO:2194, SEQ ID NO:2196, SEQ ID NO:2198, SEQ ID NO:2200, SEQ ID NO:2202, SEQ ID NO:2204, SEQ ID NO:2206, SEQ ID NO:2208, SEQ ID NO:2210, SEQ ID NO:2212, SEQ ID NO:2214, SEQ ID NO:2216, SEQ ID NO:2218, SEQ ID NO:2220, SEQ ID NO:2222, SEQ ID NO:2224, SEQ ID NO:2226, SEQ ID NO:2228, SEQ ID NO:2230, SEQ ID NO:2232, SEQ ID NO:2234, SEQ ID NO:2236, SEQ ID NO:2238, SEQ ID NO:2240, SEQ ID NO:2242, SEQ ID NO:2244, SEQ ID NO:2246, SEQ ID NO:2248, SEQ ID NO:2250, SEQ ID NO:2252, SEQ ID NO:2254, SEQ ID NO:2256, SEQ ID NO:2258, SEQ ID NO:2260, SEQ ID NO:2262, SEQ ID NO:2264, SEQ ID NO:2266, SEQ ID NO:2268, SEQ ID NO:2270, SEQ ID NO:2272, SEQ ID NO:2274, SEQ ID NO:2276, SEQ ID NO:2278, SEQ ID NO:2280, SEQ ID NO:2282, SEQ ID NO:2284, SEQ ID NO:2286, SEQ ID NO:2288, SEQ ID NO:2290, SEQ ID NO:2292, SEQ ID NO:2294, SEQ ID NO:2296, SEQ ID NO:2298, SEQ ID NO:2300, SEQ ID NO:2302, SEQ ID NO:2304, SEQ ID NO:2306, SEQ ID NO:2308, SEQ ID NO:2310, SEQ ID NO:2312, SEQ ID NO:2314, SEQ ID NO:2316, SEQ ID NO:2318, SEQ ID NO:2320, SEQ ID NO:2322, SEQ ID NO:2324, SEQ ID NO:2326, SEQ ID NO:2328, SEQ ID NO:2330, SEQ ID NO:2332, SEQ ID NO:2334, SEQ ID NO:2336, SEQ ID NO:2338, SEQ ID NO:2340, SEQ ID NO:2342, SEQ ID NO:2344, SEQ ID NO:2346, and SEQ ID NO:2348, where a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.
 6. A plant cell comprising an exogenous nucleic acid said exogenous nucleic acid comprising a regulatory region operably linked to a nucleotide sequence having 95 percent or greater sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:101, SEQ ID NO:103, SEQ ID NO:105, SEQ ID NO:107, SEQ ID NO:109, SEQ ID NO:113, SEQ ID NO:118, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:129, SEQ ID NO:133, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:148, SEQ ID NO:150, SEQ ID NO:156, SEQ ID NO:158, SEQ ID NO:160, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:169, SEQ ID NO:171, SEQ ID NO:177, SEQ ID NO:195, SEQ ID NO:197, SEQ ID NO:216, SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:252, SEQ ID NO:254, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:261, SEQ ID NO:266, SEQ ID NO:268, SEQ ID NO:271, SEQ ID NO:274, SEQ ID NO:278, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:288, SEQ ID NO:291, SEQ ID NO:293, SEQ ID NO:299, SEQ ID NO:301, SEQ ID NO:303, SEQ ID NO:305, SEQ ID NO:307, SEQ ID NO:314, SEQ ID NO:317, SEQ ID NO:320, SEQ ID NO:322, SEQ ID NO:324, SEQ ID NO:327, SEQ ID NO:329, SEQ ID NO:331, SEQ ID NO:333, SEQ ID NO:336, SEQ ID NO:338, SEQ ID NO:342, SEQ ID NO:344, SEQ ID NO:346, SEQ ID NO:352, SEQ ID NO:354, SEQ ID NO:356, SEQ ID NO:360, SEQ ID NO:369, SEQ ID NO:371, SEQ ID NO:373, SEQ ID NO:376, SEQ ID NO:378, SEQ ID NO:380, SEQ ID NO:386, SEQ ID NO:390, SEQ ID NO:393, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID NO:416, SEQ ID NO:431, SEQ ID NO:435, SEQ ID NO:437, SEQ ID NO:439, SEQ ID NO:441, SEQ ID NO:444, SEQ ID NO:448, SEQ ID NO:450, SEQ ID NO:453, SEQ ID NO:458, SEQ ID NO:460, SEQ ID NO:464, SEQ ID NO:469, SEQ ID NO:472, SEQ ID NO:474, SEQ ID NO:477, SEQ ID NO:482, SEQ ID NO:486, SEQ ID NO:489, SEQ ID NO:491, SEQ ID NO:493, SEQ ID NO:495, SEQ ID NO:500, SEQ ID NO:503, SEQ ID NO:507, SEQ ID NO:509, SEQ ID NO:515, SEQ ID NO:517, SEQ ID NO:519, SEQ ID NO:523, SEQ ID NO:525, SEQ ID NO:528, SEQ ID NO:534, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:540, SEQ ID NO:542, SEQ ID NO:544, SEQ ID NO:547, SEQ ID NO:552, SEQ ID NO:554, SEQ ID NO:562, SEQ ID NO:565, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:573, SEQ ID NO:577, SEQ ID NO:580, SEQ ID NO:582, SEQ ID NO:584, SEQ ID NO:589, SEQ ID NO:592, SEQ ID NO:595, SEQ ID NO:598, SEQ ID NO:600, SEQ ID NO:602, SEQ ID NO:605, SEQ ID NO:607, SEQ ID NO:609, SEQ ID NO:611, SEQ ID NO:613, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:637, SEQ ID NO:649, SEQ ID NO:651, SEQ ID NO:655, SEQ ID NO:658, SEQ ID NO:660, SEQ ID NO:664, SEQ ID NO:670, SEQ ID NO:674, SEQ ID NO:677, SEQ ID NO:679, SEQ ID NO:681, SEQ ID NO:683, SEQ ID NO:685, SEQ ID NO:688, SEQ ID NO:694, SEQ ID NO:697, SEQ ID NO:699, SEQ ID NO:702, SEQ ID NO:704, SEQ ID NO:706, SEQ ID NO:708, SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:717, SEQ ID NO:719, SEQ ID NO:721, SEQ ID NO:723, SEQ ID NO:729, SEQ ID NO:736, SEQ ID NO:741, SEQ ID NO:743, SEQ ID NO:746, SEQ ID NO:752, SEQ ID NO:754, SEQ ID NO:759, SEQ ID NO:764, SEQ ID NO:778, SEQ ID NO:780, SEQ ID NO:785, SEQ ID NO:789, SEQ ID NO:792, SEQ ID NO:795, SEQ ID NO:797, SEQ ID NO:799, SEQ ID NO:801, SEQ ID NO:807, SEQ ID NO:810, SEQ ID NO:813, SEQ ID NO:815, SEQ ID NO:819, SEQ ID NO:821, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:829, SEQ ID NO:832, SEQ ID NO:834, SEQ ID NO:837, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:848, SEQ ID NO:851, SEQ ID NO:854, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:864, SEQ ID NO:867, SEQ ID NO:884, SEQ ID NO:889, SEQ ID NO:891, SEQ ID NO:893, SEQ ID NO:895, SEQ ID NO:897, SEQ ID NO:899, SEQ ID NO:903, SEQ ID NO:906, SEQ ID NO:911, SEQ ID NO:913, SEQ ID NO:916, SEQ ID NO:918, SEQ ID NO:920, SEQ ID NO:926, SEQ ID NO:928, SEQ ID NO:933, SEQ ID NO:935, SEQ ID NO:937, SEQ ID NO:942, SEQ ID NO:944, SEQ ID NO:958, SEQ ID NO:963, SEQ ID NO:965, SEQ ID NO:967, SEQ ID NO:972, SEQ ID NO:974, SEQ ID NO:979, SEQ ID NO:981, SEQ ID NO:993, SEQ ID NO:1006, SEQ ID NO:1010, SEQ ID NO:1015, SEQ ID NO:1027, SEQ ID NO:1030, SEQ ID NO:1034, SEQ ID NO:1049, SEQ ID NO:1051, SEQ ID NO:1054, SEQ ID NO:1057, SEQ ID NO:1059, SEQ ID NO:1061, SEQ ID NO:1063, SEQ ID NO:1067, SEQ ID NO:1070, SEQ ID NO:1077, SEQ ID NO:1080, SEQ ID NO:1082, SEQ ID NO:1084, SEQ ID NO:1086, SEQ ID NO:1090, SEQ ID NO:1093, SEQ ID NO:1095, SEQ ID NO:1097, SEQ ID NO:1103, SEQ ID NO:1108, SEQ ID NO:1116, SEQ ID NO:1121, SEQ ID NO:1124, SEQ ID NO:1128, SEQ ID NO:1130, SEQ ID NO:1133, SEQ ID NO:1135, SEQ ID NO:1138, SEQ ID NO:1142, SEQ ID NO:1148, SEQ ID NO:1155, SEQ ID NO:1158, SEQ ID NO:1160, SEQ ID NO:1162, SEQ ID NO:1164, SEQ ID NO:1170, SEQ ID NO:1172, SEQ ID NO:1175, SEQ ID NO:1182, SEQ ID NO:1184, SEQ ID NO:1208, SEQ ID NO:1210, SEQ ID NO:1212, SEQ ID NO:1214, SEQ ID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1236, SEQ ID NO:1238, SEQ ID NO:1240, SEQ ID NO:1242, SEQ ID NO:1244, SEQ ID NO:1246, SEQ ID NO:1248, SEQ ID NO:1250, SEQ ID NO:1252, SEQ ID NO:1254, SEQ ID NO:1256, SEQ ID NO:1258, SEQ ID NO:1260, SEQ ID NO:1262, SEQ ID NO:1264, SEQ ID NO:1266, SEQ ID NO:1268, SEQ ID NO:1270, SEQ ID NO:1272, SEQ ID NO:1274, SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1282, SEQ ID NO:1284, SEQ ID NO:1291, SEQ ID NO:1293, SEQ ID NO:1295, SEQ ID NO:1297, SEQ ID NO:1299, SEQ ID NO:1301, SEQ ID NO:1310, SEQ ID NO:1312, SEQ ID NO:1314, SEQ ID NO:1316, SEQ ID NO:1318, SEQ ID NO:1320, SEQ ID NO:1322, SEQ ID NO:1324, SEQ ID NO:1326, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1332, SEQ ID NO:1334, SEQ ID NO:1336, SEQ ID NO:1338, SEQ ID NO:1340, SEQ ID NO:1342, SEQ ID NO:1344, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1356, SEQ ID NO:1358, SEQ ID NO:1360, SEQ ID NO:1368, SEQ ID NO:1370, SEQ ID NO:1372, SEQ ID NO:1374, SEQ ID NO:1376, SEQ ID NO:1378, SEQ ID NO:1380, SEQ ID NO:1382, SEQ ID NO:1384, SEQ ID NO:1386, SEQ ID NO:1388, SEQ ID NO:1390, SEQ ID NO:1392, SEQ ID NO:1394, SEQ ID NO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1402, SEQ ID NO:1404, SEQ ID NO:1411, SEQ ID NO:1413, SEQ ID NO:1416, SEQ ID NO:1418, SEQ ID NO:1420, SEQ ID NO:1422, SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1434, SEQ ID NO:1435, SEQ ID NO:1443, SEQ ID NO:1464, SEQ ID NO:1466, SEQ ID NO:1468, SEQ ID NO:1470, SEQ ID NO:1472, SEQ ID NO:1474, SEQ ID NO:1476, SEQ ID NO:1478, SEQ ID NO:1480, SEQ ID NO:1482, SEQ ID NO:1484, SEQ ID NO:1486, SEQ ID NO:1492, SEQ ID NO:1501, SEQ ID NO:1503, SEQ ID NO:1517, SEQ ID NO:1519, SEQ ID NO:1521, SEQ ID NO:1523, SEQ ID NO:1525, SEQ ID NO:1527, SEQ ID NO:1535, SEQ ID NO:1537, SEQ ID NO:1539, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1549, SEQ ID NO:1551, SEQ ID NO:1553, SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1563, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID NO:1569, SEQ ID NO:1572, SEQ ID NO:1574, SEQ ID NO:1576, SEQ ID NO:1578, SEQ ID NO:1580, SEQ ID NO:1582, SEQ ID NO:1584, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1594, SEQ ID NO:1609, SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1619, SEQ ID NO:1623, SEQ ID NO:1625, SEQ ID NO:1627, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1636, SEQ ID NO:1652, SEQ ID NO:1656, SEQ ID NO:1658, SEQ ID NO:1660, SEQ ID NO:1662, SEQ ID NO:1664, SEQ ID NO:1666, SEQ ID NO:1668, SEQ ID NO:1670, SEQ ID NO:1672, SEQ ID NO:1674, SEQ ID NO:1680, SEQ ID NO:1682, SEQ ID NO:1691, SEQ ID NO:1693, SEQ ID NO:1695, SEQ ID NO:1697, SEQ ID NO:1699, SEQ ID NO:1701, SEQ ID NO:1703, SEQ ID NO:1705, SEQ ID NO:1707, SEQ ID NO:1709, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1715, SEQ ID NO:1717, SEQ ID NO:1719, SEQ ID NO:1721, SEQ ID NO:1723, SEQ ID NO:1725, SEQ ID NO:1727, SEQ ID NO:1732, SEQ ID NO:1734, SEQ ID NO:1748, SEQ ID NO:1751, SEQ ID NO:1766, SEQ ID NO:1776, SEQ ID NO:1778, SEQ ID NO:1780, SEQ ID NO:1782, SEQ ID NO:1784, SEQ ID NO:1805, SEQ ID NO:1821, SEQ ID NO:1823, SEQ ID NO:1825, SEQ ID NO:1827, SEQ ID NO:1829, SEQ ID NO:1831, SEQ ID NO:1833, SEQ ID NO:1835, SEQ ID NO:1837, SEQ ID NO:1839, SEQ ID NO:1841, SEQ ID NO:1843, SEQ ID NO:1845, SEQ ID NO:1847, SEQ ID NO:1849, SEQ ID NO:1851, SEQ ID NO:1853, SEQ ID NO:1855, SEQ ID NO:1857, SEQ ID NO:1859, SEQ ID NO:1861, SEQ ID NO:1863, SEQ ID NO:1865, SEQ ID NO:1867, SEQ ID NO:1869, SEQ ID NO:1871, SEQ ID NO:1873, SEQ ID NO:1875, SEQ ID NO:1877, SEQ ID NO:1879, SEQ ID NO:1881, SEQ ID NO:1883, SEQ ID NO:1885, SEQ ID NO:1887, SEQ ID NO:1889, SEQ ID NO:1891, SEQ ID NO:1896, SEQ ID NO:1898, SEQ ID NO:1900, SEQ ID NO:1903, SEQ ID NO:1905, SEQ ID NO:1907, SEQ ID NO:1919, SEQ ID NO:1920, SEQ ID NO:2060, SEQ ID NO:2062, SEQ ID NO:2064, SEQ ID NO:2084, SEQ ID NO:2088, SEQ ID NO:2090, SEQ ID NO:2092, SEQ ID NO:2094, SEQ ID NO:2096, SEQ ID NO:2098, SEQ ID NO:2100, SEQ ID NO:2102, SEQ ID NO:2104, SEQ ID NO:2106, SEQ ID NO:2108, SEQ ID NO:2110, SEQ ID NO:2112, SEQ ID NO:2114, SEQ ID NO:2116, SEQ ID NO:2118, SEQ ID NO:2120, SEQ ID NO:2122, SEQ ID NO:2124, SEQ ID NO:2126, SEQ ID NO:2128, SEQ ID NO:2130, SEQ ID NO:2132, SEQ ID NO:2134, SEQ ID NO:2136, SEQ ID NO:2138, SEQ ID NO:2140, SEQ ID NO:2142, SEQ ID NO:2144, SEQ ID NO:2146, SEQ ID NO:2148, SEQ ID NO:2150, SEQ ID NO:2152, SEQ ID NO:2154, SEQ ID NO:2156, SEQ ID NO:2158, SEQ ID NO:2160, SEQ ID NO:2161, SEQ ID NO:2163, SEQ ID NO:2165, SEQ ID NO:6167, SEQ ID NO:2169, SEQ ID NO:2171, SEQ ID NO:2173, SEQ ID NO:2175, SEQ ID NO:2177, SEQ ID NO:2179, SEQ ID NO:2181, SEQ ID NO:2183, SEQ ID NO:2185, SEQ ID NO:2187, SEQ ID NO:2189, SEQ ID NO:2191, SEQ ID NO:2193, SEQ ID NO:2195, SEQ ID NO:2197, SEQ ID NO:2199, SEQ ID NO:2201, SEQ ID NO:2203, SEQ ID NO:2205, SEQ ID NO:2207, SEQ ID NO:2209, SEQ ID NO:2211, SEQ ID NO:2213, SEQ ID NO:2215, SEQ ID NO:2217, SEQ ID NO:2219, SEQ ID NO:2221, SEQ ID NO:2223, SEQ ID NO:2225, SEQ ID NO:2227, SEQ ID NO:2229, SEQ ID NO:2231, SEQ ID NO:2233, SEQ ID NO:2235, SEQ ID NO:2237, SEQ ID NO:2239, SEQ ID NO:2241, SEQ ID NO:2243, SEQ ID NO:2245, SEQ ID NO:2247, SEQ ID NO:2249, SEQ ID NO:2251, SEQ ID NO:2253, SEQ ID NO:2255, SEQ ID NO:2257, SEQ ID NO:2259, SEQ ID NO:2261, SEQ ID NO:2263, SEQ ID NO:2265, SEQ ID NO:2267, SEQ ID NO:2269, SEQ ID NO:2271, SEQ ID NO:2273, SEQ ID NO:2275, SEQ ID NO:2277, SEQ ID NO:2279, SEQ ID NO:2281, SEQ ID NO:2283, SEQ ID NO:2285, SEQ ID NO:2287, SEQ ID NO:2289, SEQ ID NO:2291, SEQ ID NO:2293, SEQ ID NO:2295, SEQ ID NO:2297, SEQ ID NO:2299, SEQ ID NO:2301, SEQ ID NO:2303, SEQ ID NO:2305, SEQ ID NO:2307, SEQ ID NO:2309, SEQ ID NO:2311, SEQ ID NO:2313, SEQ ID NO:2315, SEQ ID NO:2317, SEQ ID NO:2319, SEQ ID NO:2321, SEQ ID NO:2323, SEQ ID NO:2325, SEQ ID NO:2327, SEQ ID NO:2329, SEQ ID NO:2331, SEQ ID NO:2333, SEQ ID NO:2335, SEQ ID NO:2337, SEQ ID NO:2339, SEQ ID NO:2341, SEQ ID NO:2343, SEQ ID NO:2345, SEQ ID NO:2347, and SEQ ID NO:2349-2690, or a fragment thereof, wherein a tissue of a plant produced from the plant cell has a difference in lignin content as compared to the corresponding lignin content in tissue of a control plant that does not comprise the nucleic acid.
 7. The plant cell of claim 5, wherein said regulatory region is involved in lignin or cellulose biosynthesis.
 8. The plant cell of claim 7, wherein said regulatory region is selected from the group consisting of SEQ ID NOs:1909-1918.
 9. The plant cell of claim 5, wherein said regulatory region is not associated with said polypeptide.
 10. The plant cell of claim 5, wherein said regulatory region is a promoter.
 11. The plant cell of claim 10, wherein said promoter is a tissue-preferential promoter.
 12. (canceled)
 13. The plant cell of claim 10, wherein said promoter is a cell type-preferential promoter.
 14. (canceled)
 15. The plant cell of claim 10, wherein said promoter is an inducible promoter.
 16. The plant cell of claim 5, wherein said plant cell is capable of producing one or more lignin monomers.
 17. The plant cell of claim 5, wherein said polypeptide modulates expression of an endogenous gene involved in lignin biosynthesis in said cell. 18.-19. (canceled)
 20. The plant cell of claim 17, wherein said modulation is an increase in expression of said endogenous gene.
 21. The plant cell of claim 5, wherein said plant cell further comprises a sequence of interest operably linked to a regulatory region associated with said polypeptide.
 22. (canceled)
 23. The plant cell of claim 16, wherein said plant is from a genus selected from the group consisting of Acer, Aesculus, Afzelia, Agrostis, Alnus, Avena, Cannabis, Carya, Cinnamomum, Coffea, Eucalyptus, Festuca, Fraxinus, Hordeum, Juglans, Lolium, Medicago, Milium, Miscanthus, Panicum, Pinus, Poa, Populus, Prunus, Quercus, Saccharum, Simarouba, Sorghum, Trifolium, Triticum, Vitis, and Zea.
 24. The plant cell of claim 22, wherein said plant is a species selected from Miscanthus hybrid (Miscanthus×giganteus), Miscanthus sinensis, Miscanthus sacchariflorus, Panicum virgatum, and Populus trichocarpa. 25.-26. (canceled)
 27. The plant cell of claim 21, wherein expression of said sequence of interest inhibits expression of an endogenous gene involved in lignin biosynthesis.
 28. (canceled)
 29. The plant cell of claim 27, wherein said sequence of interest is transcribed into an interfering RNA. 30.-32. (canceled)
 33. The plant cell of claim 27, wherein said plant cell is from a genus selected from the group consisting of Acer, Aesculus, Afzelia, Agrostis, Alnus, Avena, Cannabis, Carya, Cinnamomum, Coffea, Eucalyptus, Festuca, Fraxinus, Hordeum, Juglans, Lolium, Medicago, Milium, Miscanthus, Panicum, Pinus, Poa, Populus, Prunus, Quercus, Saccharum, Simarouba, Sorghum, Trifolium, Triticum, Vitis, and Zea. 34.-37. (canceled)
 38. The plant cell of claim 21, wherein said polypeptide-regulatory region association is effective for increasing lignin biosynthesis in said cell.
 39. The plant cell of claim 21, wherein said regulatory protein-regulatory region association is effective for decreasing lignin biosynthesis in said cell. 40.-65. (canceled) 